Back to Long Tests report for BioC 3.20

This page was generated on 2025-01-25 23:55 -0500 (Sat, 25 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4746
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4494
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4517
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: 2025-01-25 09:55 -0500 (Sat, 25 Jan 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 -0500 (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: 2025-01-25 16:02:17 -0500 (Sat, 25 Jan 2025)
EndedAt: 2025-01-25 16:03:35 -0500 (Sat, 25 Jan 2025)
EllapsedTime: 78.0 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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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> # 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 [2025-01-25 16:03:30.905][biodb::testContext]
biodb.INFO [2025-01-25 16:03:30.909][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-25 16:03:30.910][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-01-25 16:03:30.911][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-25 16:03:30.912][biodb::testContext]
biodb.INFO [2025-01-25 16:03:30.919][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-01-25 16:03:30.921][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-01-25 16:03:30.929][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-25 16:03:30.930][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-25 16:03:30.931][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-25 16:03:30.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:30.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:30.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:30.936][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-25 16:03:30.961][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-25 16:03:30.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:30.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:30.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:30.965][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-25 16:03:30.967][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-25 16:03:30.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:30.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:30.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:30.971][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-25 16:03:30.972][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-25 16:03:30.973][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-25 16:03:30.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:30.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:30.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:30.978][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-25 16:03:30.980][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-25 16:03:30.981][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-25 16:03:30.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:30.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:30.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:30.985][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-25 16:03:30.987][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-25 16:03:30.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:30.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:30.990][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[2025-01-25 16:03:30.991][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-25 16:03:30.993][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-25 16:03:30.994][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-25 16:03:30.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:30.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:30.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:30.998][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-25 16:03:31.000][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-25 16:03:31.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.003][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[2025-01-25 16:03:31.004][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-25 16:03:31.006][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-25 16:03:31.007][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-25 16:03:31.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.011][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-25 16:03:31.013][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-25 16:03:31.014][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-25 16:03:31.015][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-25 16:03:31.016][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-25 16:03:31.018][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-25 16:03:31.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.022][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-25 16:03:31.023][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-25 16:03:31.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.028][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-25 16:03:31.029][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-25 16:03:31.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.034][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-25 16:03:31.035][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-25 16:03:31.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.040][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-25 16:03:31.041][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-25 16:03:31.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.046][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-25 16:03:31.047][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-25 16:03:31.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.052][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-25 16:03:31.053][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-25 16:03:31.065][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-25 16:03:31.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.069][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-25 16:03:31.071][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-25 16:03:31.072][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-25 16:03:31.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.079][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-25 16:03:31.125][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:31.154][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-01-25 16:03:31.155][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:31.156][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:03:31.157][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:31.159][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-25 16:03:31.160][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:31.161][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:03:31.162][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-25 16:03:31.164][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:03:31.165][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:31.166][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-25 16:03:31.168][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:03:31.169][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:31.170][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:31.171][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-25 16:03:31.171][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-25 16:03:31.171][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-25 16:03:31.171][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-25 16:03:31.171][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-25 16:03:31.173][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-25 16:03:31.174][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:03:31.175][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:03:31.176][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:03:31.178][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:03:31.179][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:03:31.180][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:03:31.181][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:31.182][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:03:31.183][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:03:31.184][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:31.186][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:31.187][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-25 16:03:31.189][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:31.190][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-25 16:03:31.192][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:31.193][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:03:31.194][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:31.195][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-25 16:03:31.196][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:31.198][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:03:31.199][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-25 16:03:31.200][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:03:31.201][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:31.202][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-25 16:03:31.204][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:03:31.205][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:31.206][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:31.207][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-25 16:03:31.207][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-25 16:03:31.207][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-25 16:03:31.207][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-25 16:03:31.207][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-25 16:03:31.209][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-25 16:03:31.210][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:03:31.211][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:03:31.212][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:03:31.213][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:03:31.214][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:03:31.215][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:03:31.217][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:31.218][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:03:31.219][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:03:31.220][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:31.221][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:31.223][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-25 16:03:31.225][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:31.226][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-01-25 16:03:31.227][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:31.229][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:03:31.230][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:31.231][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-25 16:03:31.232][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:31.234][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:03:31.235][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-25 16:03:31.236][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:03:31.237][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:31.239][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-25 16:03:31.240][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:03:31.241][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:31.242][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:31.243][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:31.245][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-25 16:03:31.246][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:03:31.247][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:03:31.248][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:03:31.249][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:03:31.250][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:03:31.252][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:03:31.253][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:31.254][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:03:31.255][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:03:31.256][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:31.258][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:31.259][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-25 16:03:31.261][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:31.262][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-25 16:03:31.264][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:31.265][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:03:31.267][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:31.268][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-25 16:03:31.269][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:31.270][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:03:31.271][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-25 16:03:31.273][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:03:31.274][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:31.275][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-25 16:03:31.276][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:03:31.277][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:31.279][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:31.280][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:31.281][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-25 16:03:31.282][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:03:31.283][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:03:31.285][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:03:31.286][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:03:31.287][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:03:31.288][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:03:31.289][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:31.290][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:03:31.291][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:03:31.293][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:31.294][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:31.298][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-25 16:03:31.299][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.397][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-25 16:03:31.402][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-25 16:03:31.404][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-25 16:03:31.406][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-25 16:03:31.407][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-25 16:03:31.409][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-25 16:03:31.411][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-25 16:03:31.412][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-25 16:03:31.414][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-25 16:03:31.416][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-25 16:03:31.417][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-25 16:03:31.419][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-25 16:03:31.421][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-25 16:03:31.422][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-25 16:03:31.424][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-25 16:03:31.426][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-25 16:03:31.428][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-25 16:03:31.429][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-25 16:03:31.431][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-25 16:03:31.433][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-25 16:03:31.435][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-25 16:03:31.436][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-25 16:03:31.438][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-25 16:03:31.440][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-25 16:03:31.442][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-25 16:03:31.443][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-25 16:03:31.445][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-25 16:03:31.447][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-25 16:03:31.448][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-25 16:03:31.450][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-25 16:03:31.452][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-25 16:03:31.454][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-25 16:03:31.456][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-25 16:03:31.457][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-25 16:03:31.459][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-25 16:03:31.461][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-25 16:03:31.463][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-25 16:03:31.465][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-25 16:03:31.466][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-25 16:03:31.468][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-25 16:03:31.470][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-25 16:03:31.472][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-25 16:03:31.473][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-25 16:03:31.475][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-25 16:03:31.477][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-25 16:03:31.479][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-25 16:03:31.480][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-25 16:03:31.482][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-25 16:03:31.484][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-25 16:03:31.486][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-25 16:03:31.488][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-25 16:03:31.490][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-25 16:03:31.492][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-25 16:03:31.494][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-25 16:03:31.495][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-25 16:03:31.497][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-25 16:03:31.499][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-25 16:03:31.501][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-25 16:03:31.502][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-25 16:03:31.504][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-25 16:03:31.506][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-25 16:03:31.507][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-25 16:03:31.509][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-25 16:03:31.511][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-25 16:03:31.512][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-25 16:03:31.514][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-25 16:03:31.516][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-25 16:03:31.518][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-25 16:03:31.519][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-25 16:03:31.521][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-25 16:03:31.523][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-25 16:03:31.524][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-25 16:03:31.526][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-25 16:03:31.528][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-25 16:03:31.529][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-25 16:03:31.531][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-25 16:03:31.533][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-25 16:03:31.535][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-25 16:03:31.536][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-25 16:03:31.538][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-25 16:03:31.540][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-25 16:03:31.541][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-25 16:03:31.543][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-25 16:03:31.551][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-25 16:03:31.553][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-01-25 16:03:31.556][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-25 16:03:31.557][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.559][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:31.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:31.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:31.577][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:31.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.586][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[2025-01-25 16:03:31.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:31.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:31.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:31.597][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:31.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:31.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:31.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:31.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:31.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:31.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:31.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:31.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:31.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:31.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:31.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:31.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:31.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:31.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:31.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:31.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:31.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:31.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:31.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:31.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:31.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:31.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:31.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.686][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:31.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:31.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:31.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:31.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:31.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:31.704][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-01-25 16:03:31.717][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-01-25 16:03:31.719][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:31.720][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-01-25 16:03:31.722][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:31.723][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:03:31.724][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:31.725][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-01-25 16:03:31.726][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:31.728][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:03:31.729][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-01-25 16:03:31.730][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:03:31.731][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:31.733][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-01-25 16:03:31.734][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:03:31.735][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-01-25 16:03:31.735][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-01-25 16:03:31.735][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-01-25 16:03:31.735][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-01-25 16:03:31.735][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-01-25 16:03:31.735][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-01-25 16:03:31.735][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-01-25 16:03:31.736][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:31.738][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:31.739][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-25 16:03:31.740][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:03:31.741][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:03:31.742][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:03:31.743][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:03:31.744][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:03:31.746][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:03:31.747][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-01-25 16:03:31.747][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-01-25 16:03:31.747][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-01-25 16:03:31.747][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-01-25 16:03:31.748][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:03:31.749][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:03:31.750][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:31.752][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:31.759][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-01-25 16:03:31.782][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-01-25 16:03:31.783][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-01-25 16:03:31.788][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-01-25 16:03:31.792][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-01-25 16:03:31.796][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-25 16:03:31.798][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-25 16:03:31.799][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-01-25 16:03:31.801][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-01-25 16:03:31.802][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-01-25 16:03:31.803][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-01-25 16:03:31.841][biodb::testThat]
biodb.INFO [2025-01-25 16:03:31.843][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-01-25 16:03:31.844][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:03:31.845][biodb::testThat]
biodb.TRACE[2025-01-25 16:03:31.849][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[2025-01-25 16:03:31.851][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-01-25 16:03:31.855][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-01-25 16:03:31.863][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-25 16:03:31.864][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:31.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:31.881][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:31.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:31.883][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:31.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-25 16:03:31.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:31.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:31.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:31.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:31.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:31.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:31.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:31.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:31.934][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:31.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:31.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:31.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:31.974][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:31.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:31.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:31.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:31.979][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:31.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:31.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:31.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:31.984][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:31.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:31.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:31.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:31.990][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:31.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:31.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:31.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:31.996][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:31.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:31.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:31.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.001][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:32.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:32.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.006][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:32.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:32.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.012][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:32.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:32.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.017][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:32.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:32.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.027][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:32.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:32.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:03:32.114][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-01-25 16:03:32.117][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-25 16:03:32.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-25 16:03:32.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.122][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-25 16:03:32.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-25 16:03:32.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.127][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-25 16:03:32.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-25 16:03:32.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.132][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-25 16:03:32.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-25 16:03:32.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.175][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:32.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:32.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.218][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:32.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:32.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.223][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:32.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:32.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.228][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:32.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:32.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.262][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.264][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.265][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.266][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.283][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:32.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:32.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.288][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:32.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:32.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.294][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:32.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:32.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.298][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:32.300][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:32.301][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.302][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.303][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:32.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:32.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.318][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:32.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:32.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:32.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:32.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.329][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:32.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:32.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.334][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:32.335][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:32.336][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.338][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.339][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:32.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:32.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.354][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:32.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:32.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.359][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:32.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:32.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.364][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:32.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:32.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.369][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:32.371][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:32.372][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.373][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.374][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:32.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:32.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.390][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:32.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:32.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.395][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:32.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:32.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.400][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:32.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:32.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.405][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:32.406][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:32.407][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.408][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.410][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:32.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:32.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.426][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.431][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.433][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.434][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.440][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:32.442][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:32.443][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.444][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.450][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:32.452][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:32.453][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.454][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.460][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:32.462][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:32.463][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.464][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.470][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:32.472][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:32.473][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.474][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.498][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[2025-01-25 16:03:32.547][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-01-25 16:03:32.548][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-01-25 16:03:32.550][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-25 16:03:32.551][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:32.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:32.558][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:32.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:32.561][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:32.562][FUN] Functions in observer BiodbConfig: [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[2025-01-25 16:03:32.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.615][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:03:32.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:03:32.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.620][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:03:32.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:03:32.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.625][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:32.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:32.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.630][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:32.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:32.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.636][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:32.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:32.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.641][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:32.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:32.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.646][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:32.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:32.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.651][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:32.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:32.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.656][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:32.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:32.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.661][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:32.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:32.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.666][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:32.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:32.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.671][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:32.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:32.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.676][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:32.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:32.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.682][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:32.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:32.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.687][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:32.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:32.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.692][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:32.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:32.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.697][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:32.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:32.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.703][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:32.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:32.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.708][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:32.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:32.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.718][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:32.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:32.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.748][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:03:32.753][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-01-25 16:03:32.781][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-25 16:03:32.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-25 16:03:32.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.786][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-25 16:03:32.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-25 16:03:32.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.794][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-25 16:03:32.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-25 16:03:32.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.799][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-25 16:03:32.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-25 16:03:32.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.815][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:32.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:32.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.856][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:32.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:32.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.861][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:32.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:32.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.866][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:32.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:32.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.907][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.908][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.909][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.910][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:32.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:32.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.926][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:03:32.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:03:32.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.931][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:03:32.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:03:32.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.936][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:03:32.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:03:32.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.941][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:03:32.942][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:03:32.943][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.944][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.945][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:03:32.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:03:32.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.960][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:32.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:32.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.965][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:32.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:32.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.974][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:32.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:32.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.979][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:32.980][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:32.981][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.982][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.983][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:32.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:32.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:32.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:32.998][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:33.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:33.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.004][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:33.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:33.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.009][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:33.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:33.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.014][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:33.015][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:33.017][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.018][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.019][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:33.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:33.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.034][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:33.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:33.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.039][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:33.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:33.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.044][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:33.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:33.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.049][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:33.050][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:33.052][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.053][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.054][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:33.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:33.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.069][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:33.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:33.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.074][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:33.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:33.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.079][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:33.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:33.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.084][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:33.086][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:33.087][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.088][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.089][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:33.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:33.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.104][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:33.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:33.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.109][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:33.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:33.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.114][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:33.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:33.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.119][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:33.120][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:33.121][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.123][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.124][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:33.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:33.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.139][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:33.140][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:33.141][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.142][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.149][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:03:33.150][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:03:33.151][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.153][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.163][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:33.164][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:33.165][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.167][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.173][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:33.174][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:33.175][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.176][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.182][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:33.184][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:33.185][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.186][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.192][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:33.193][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:33.195][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.196][ef$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.202][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:33.203][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:33.204][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.206][ef$get] fields variable is a list.
biodb.INFO [2025-01-25 16:03:33.216][biodb::testThat]
biodb.INFO [2025-01-25 16:03:33.217][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-01-25 16:03:33.218][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:03:33.219][biodb::testThat]
biodb.DEBUG[2025-01-25 16:03:33.222][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-01-25 16:03:33.230][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-01-25 16:03:33.235][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-01-25 16:03:33.236][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.TRACE[2025-01-25 16:03:33.239][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2025-01-25 16:03:33.240][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2025-01-25 16:03:33.243][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[2025-01-25 16:03:33.244][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2025-01-25 16:03:33.246][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2025-01-25 16:03:33.247][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2025-01-25 16:03:33.249][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-25 16:03:33.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:33.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:33.257][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:33.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:33.260][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:33.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-25 16:03:33.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:33.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:33.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:33.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:33.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.284][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:33.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:33.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.289][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:33.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:33.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.294][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:33.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:33.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.299][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:33.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:33.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.305][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:33.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:33.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.310][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:33.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:33.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.316][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:33.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:33.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.321][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:33.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:33.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.327][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:33.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:33.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.332][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:33.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:33.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:33.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:33.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.342][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:33.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:33.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:33.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:33.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:33.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:33.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:33.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:33.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:03:33.367][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-25 16:03:33.368][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:33.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:33.376][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:33.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:33.378][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:33.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-25 16:03:33.394][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:33.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:33.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:33.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:33.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.406][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:03:33.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:03:33.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.411][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-25 16:03:33.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-25 16:03:33.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.417][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:33.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:33.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.422][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-25 16:03:33.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-25 16:03:33.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.427][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:33.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:33.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.432][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:33.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-25 16:03:33.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.437][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:33.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:33.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.442][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:33.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:33.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.447][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:33.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:33.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.452][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:33.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:33.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.457][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:33.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:33.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.462][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:33.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:33.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.467][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-25 16:03:33.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-25 16:03:33.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.473][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:33.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:33.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.478][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-25 16:03:33.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-25 16:03:33.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.484][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:33.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:33.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.489][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-25 16:03:33.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-25 16:03:33.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.495][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:33.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:33.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.500][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:33.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:33.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:33.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:33.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.510][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:33.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-25 16:03:33.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:33.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:33.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:33.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:33.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.525][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:33.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:33.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:33.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:33.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:33.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:33.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:33.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:33.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:33.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:33.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:33.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:33.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-25 16:03:33.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-25 16:03:33.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-25 16:03:33.568][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2025-01-25 16:03:33.570][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-01-25 16:03:33.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-01-25 16:03:33.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.575][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-01-25 16:03:33.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-01-25 16:03:33.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.580][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-01-25 16:03:33.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-01-25 16:03:33.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.590][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-01-25 16:03:33.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-01-25 16:03:33.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.596][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-01-25 16:03:33.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-01-25 16:03:33.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.601][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-01-25 16:03:33.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-01-25 16:03:33.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-25 16:03:33.615][biodb::testThat]
biodb.INFO [2025-01-25 16:03:33.616][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-01-25 16:03:33.618][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:03:33.619][biodb::testThat]
biodb.INFO [2025-01-25 16:03:33.627][biodb::testThat]
biodb.INFO [2025-01-25 16:03:33.628][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-01-25 16:03:33.629][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:03:33.630][biodb::testThat]
biodb.WARN [2025-01-25 16:03:33.657][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-01-25 16:03:33.683][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-01-25 16:03:33.695][biodb::testThat]
biodb.INFO [2025-01-25 16:03:33.696][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-01-25 16:03:33.698][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:03:33.699][biodb::testThat]
biodb.TRACE[2025-01-25 16:03:33.735][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-25 16:03:33.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-25 16:03:33.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.740][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-25 16:03:33.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-25 16:03:33.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.745][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-25 16:03:33.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-25 16:03:33.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.750][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-25 16:03:33.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-25 16:03:33.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.801][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-25 16:03:33.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-25 16:03:33.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.806][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-25 16:03:33.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-25 16:03:33.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.811][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-25 16:03:33.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-25 16:03:33.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-25 16:03:33.817][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-25 16:03:33.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-25 16:03:33.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-25 16:03:33.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-25 16:03:33.829][biodb::testThat]
biodb.INFO [2025-01-25 16:03:33.830][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-01-25 16:03:33.832][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:03:33.833][biodb::testThat]
biodb.INFO [2025-01-25 16:03:33.843][biodb::testThat]
biodb.INFO [2025-01-25 16:03:33.845][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-01-25 16:03:33.846][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:03:33.848][biodb::testThat]
biodb.INFO [2025-01-25 16:03:33.858][biodb::testThat]
biodb.INFO [2025-01-25 16:03:33.859][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-01-25 16:03:33.860][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:03:33.861][biodb::testThat]
biodb.INFO [2025-01-25 16:03:33.870][biodb::testThat]
biodb.INFO [2025-01-25 16:03:33.871][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-01-25 16:03:33.872][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-25 16:03:33.873][biodb::testThat]
biodb.INFO [2025-01-25 16:03:33.881][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-25 16:03:33.883][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-01-25 16:03:33.884][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-01-25 16:03:33.885][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-25 16:03:33.886][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:33.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:33.888][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:33.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:33.891][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:33.892][FUN] Functions in observer BiodbConfig: [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 [2025-01-25 16:03:33.904][biodb::testContext]
biodb.INFO [2025-01-25 16:03:33.906][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-25 16:03:33.911][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-01-25 16:03:33.912][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-25 16:03:33.913][biodb::testContext]
biodb.INFO [2025-01-25 16:03:33.916][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2025-01-25 16:03:33.918][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2025-01-25 16:03:33.922][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-25 16:03:33.923][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-25 16:03:33.925][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-25 16:03:33.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:33.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:33.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:33.929][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-25 16:03:33.930][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-25 16:03:33.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:33.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:33.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:33.935][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-25 16:03:33.936][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-25 16:03:33.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:33.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:33.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:33.941][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-25 16:03:33.942][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-25 16:03:33.943][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-25 16:03:33.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:33.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:33.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:33.948][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-25 16:03:33.949][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-25 16:03:33.951][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-25 16:03:33.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:33.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:33.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:33.955][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-25 16:03:33.960][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-25 16:03:33.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:33.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:33.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:33.965][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-25 16:03:33.966][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-25 16:03:33.968][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-25 16:03:33.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:33.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:33.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:33.972][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-25 16:03:33.973][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-25 16:03:33.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:33.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:33.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:33.978][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-25 16:03:33.979][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-25 16:03:33.980][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-25 16:03:33.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:33.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:33.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:33.985][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-25 16:03:33.986][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-25 16:03:33.987][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-25 16:03:33.989][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-25 16:03:33.990][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-25 16:03:33.991][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-25 16:03:33.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:33.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:33.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:33.996][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-25 16:03:33.997][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-25 16:03:33.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:33.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.001][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-25 16:03:34.003][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-25 16:03:34.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.007][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-25 16:03:34.008][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-25 16:03:34.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.013][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-25 16:03:34.014][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-25 16:03:34.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.018][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[2025-01-25 16:03:34.019][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-25 16:03:34.020][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-25 16:03:34.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.025][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-25 16:03:34.026][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-25 16:03:34.037][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-25 16:03:34.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.040][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[2025-01-25 16:03:34.041][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-25 16:03:34.043][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-25 16:03:34.044][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-25 16:03:34.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.049][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-25 16:03:34.051][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:34.052][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-01-25 16:03:34.053][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:34.055][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:03:34.056][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:34.057][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-25 16:03:34.058][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:34.060][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:03:34.061][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-25 16:03:34.062][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:03:34.063][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:34.064][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-25 16:03:34.066][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:03:34.067][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:34.068][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:34.069][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-25 16:03:34.069][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-25 16:03:34.069][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-25 16:03:34.069][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-25 16:03:34.069][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-25 16:03:34.071][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-25 16:03:34.072][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:03:34.073][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:03:34.074][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:03:34.075][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:03:34.076][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:03:34.078][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:03:34.079][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:34.080][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:03:34.081][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:03:34.082][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:34.084][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:34.085][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-25 16:03:34.087][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:34.089][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-25 16:03:34.090][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:34.091][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:03:34.096][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:34.098][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-25 16:03:34.099][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:34.100][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:03:34.102][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-25 16:03:34.103][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:03:34.104][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:34.105][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-25 16:03:34.107][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:03:34.108][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:34.109][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:34.110][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-25 16:03:34.110][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-25 16:03:34.110][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-25 16:03:34.110][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-25 16:03:34.110][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-25 16:03:34.112][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-25 16:03:34.113][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:03:34.114][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:03:34.115][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:03:34.116][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:03:34.117][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:03:34.119][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:03:34.120][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:34.121][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:03:34.122][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:03:34.123][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:34.124][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:34.126][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-25 16:03:34.128][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:34.129][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-01-25 16:03:34.131][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:34.132][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:03:34.133][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:34.134][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-25 16:03:34.136][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:34.137][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:03:34.138][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-25 16:03:34.139][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:03:34.140][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:34.142][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-25 16:03:34.143][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:03:34.144][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:34.145][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:34.147][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:34.148][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-25 16:03:34.149][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:03:34.150][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:03:34.151][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:03:34.152][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:03:34.153][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:03:34.155][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:03:34.156][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:34.157][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:03:34.158][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:03:34.159][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:34.161][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:34.162][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-25 16:03:34.164][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:34.165][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-25 16:03:34.167][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:34.168][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:03:34.169][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:34.170][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-25 16:03:34.171][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:34.173][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:03:34.174][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-25 16:03:34.175][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:03:34.176][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:34.178][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-25 16:03:34.179][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:03:34.180][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:34.181][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:34.182][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:34.184][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-25 16:03:34.185][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:03:34.186][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:03:34.187][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:03:34.188][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:03:34.190][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:03:34.191][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:03:34.192][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:34.193][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:03:34.194][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:03:34.195][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:34.197][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:34.198][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-25 16:03:34.199][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.270][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[2025-01-25 16:03:34.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.275][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[2025-01-25 16:03:34.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.281][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[2025-01-25 16:03:34.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.288][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.299][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-25 16:03:34.301][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-25 16:03:34.302][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-25 16:03:34.304][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-25 16:03:34.306][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-25 16:03:34.308][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-25 16:03:34.309][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-25 16:03:34.311][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-25 16:03:34.313][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-25 16:03:34.315][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-25 16:03:34.316][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-25 16:03:34.318][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-25 16:03:34.320][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-25 16:03:34.322][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-25 16:03:34.324][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-25 16:03:34.325][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-25 16:03:34.327][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-25 16:03:34.329][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-25 16:03:34.331][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-25 16:03:34.332][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-25 16:03:34.334][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-25 16:03:34.336][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-25 16:03:34.338][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-25 16:03:34.339][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-25 16:03:34.341][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-25 16:03:34.343][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-25 16:03:34.344][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-25 16:03:34.346][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-25 16:03:34.348][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-25 16:03:34.349][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-25 16:03:34.351][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-25 16:03:34.353][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-25 16:03:34.355][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-25 16:03:34.356][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-25 16:03:34.358][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-25 16:03:34.360][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-25 16:03:34.361][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-25 16:03:34.363][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-25 16:03:34.365][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-25 16:03:34.367][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-25 16:03:34.368][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-25 16:03:34.370][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-25 16:03:34.372][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-25 16:03:34.373][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-25 16:03:34.375][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-25 16:03:34.377][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-25 16:03:34.379][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-25 16:03:34.380][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-25 16:03:34.382][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-25 16:03:34.384][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-25 16:03:34.385][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-25 16:03:34.387][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-25 16:03:34.389][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-25 16:03:34.391][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-25 16:03:34.392][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-25 16:03:34.394][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-25 16:03:34.396][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-25 16:03:34.397][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-25 16:03:34.399][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-25 16:03:34.401][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-25 16:03:34.403][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-25 16:03:34.404][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-25 16:03:34.406][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-25 16:03:34.408][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-25 16:03:34.409][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-25 16:03:34.411][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-25 16:03:34.413][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-25 16:03:34.414][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-25 16:03:34.416][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-25 16:03:34.418][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-25 16:03:34.420][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-25 16:03:34.421][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-25 16:03:34.423][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-25 16:03:34.425][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-25 16:03:34.432][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-25 16:03:34.434][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-25 16:03:34.435][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-25 16:03:34.437][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-25 16:03:34.439][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-25 16:03:34.441][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-25 16:03:34.442][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-25 16:03:34.444][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-25 16:03:34.446][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-25 16:03:34.448][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-25 16:03:34.450][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2025-01-25 16:03:34.451][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-25 16:03:34.452][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.454][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:34.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:34.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:34.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:34.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:34.474][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:34.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:34.482][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:34.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:34.490][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:34.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:34.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:34.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:34.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:34.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:34.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:34.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:34.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:34.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:34.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:34.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:34.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:34.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:34.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:34.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:34.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:34.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:34.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:34.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:34.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:34.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:34.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:34.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.580][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-25 16:03:34.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:34.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:34.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-25 16:03:34.590][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-01-25 16:03:34.591][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-01-25 16:03:34.594][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:34.600][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-01-25 16:03:34.601][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:34.602][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-25 16:03:34.603][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:34.605][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-01-25 16:03:34.606][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:34.607][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-25 16:03:34.608][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-01-25 16:03:34.609][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-25 16:03:34.611][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:34.612][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-01-25 16:03:34.613][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-25 16:03:34.614][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-01-25 16:03:34.614][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-01-25 16:03:34.614][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-01-25 16:03:34.614][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-01-25 16:03:34.614][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-01-25 16:03:34.614][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-01-25 16:03:34.614][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-01-25 16:03:34.616][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-25 16:03:34.617][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:34.618][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-25 16:03:34.620][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:03:34.621][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:03:34.622][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-25 16:03:34.623][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-25 16:03:34.624][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-25 16:03:34.625][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-25 16:03:34.627][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-01-25 16:03:34.627][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-01-25 16:03:34.627][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-01-25 16:03:34.627][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-01-25 16:03:34.628][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-25 16:03:34.629][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-25 16:03:34.630][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-25 16:03:34.631][self$setPropertyValue]
biodb.DEBUG[2025-01-25 16:03:34.633][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-01-25 16:03:34.637][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-01-25 16:03:34.638][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-01-25 16:03:34.640][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-01-25 16:03:34.642][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-01-25 16:03:34.643][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-25 16:03:34.644][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-25 16:03:34.646][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-01-25 16:03:34.647][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-01-25 16:03:34.649][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-01-25 16:03:34.650][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-01-25 16:03:34.651][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-25 16:03:34.653][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-01-25 16:03:34.654][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-01-25 16:03:34.655][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-25 16:03:34.656][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-25 16:03:34.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-25 16:03:34.658][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-25 16:03:34.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-25 16:03:34.661][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-25 16:03:34.662][FUN] Functions in observer 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 
  5.769   0.328   6.084

'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 4.4.2 (2024-10-31)
* 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)