Back to Long Tests report for BioC 3.21

This page was generated on 2025-02-08 23:55 -0500 (Sat, 08 Feb 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4719
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4480
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" 4491
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 9/30HostnameOS / ArchCHECK
biodbNci 1.11.0  (landing page)
Pierrick Roger
Snapshot Date: 2025-02-08 11:09 -0500 (Sat, 08 Feb 2025)
git_url: https://git.bioconductor.org/packages/biodbNci
git_branch: devel
git_last_commit: 10e1a05
git_last_commit_date: 2024-10-29 11:09:24 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK  
palomino7Windows Server 2022 Datacenter / x64  OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK  

CHECK results for biodbNci on nebbiolo1

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: 1.11.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.11.0.tar.gz
StartedAt: 2025-02-08 16:04:08 -0500 (Sat, 08 Feb 2025)
EndedAt: 2025-02-08 16:05:09 -0500 (Sat, 08 Feb 2025)
EllapsedTime: 61.1 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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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 [2025-02-08 16:05:05.721][biodb::testContext]
biodb.INFO [2025-02-08 16:05:05.723][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-08 16:05:05.724][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-02-08 16:05:05.725][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-08 16:05:05.725][biodb::testContext]
biodb.INFO [2025-02-08 16:05:05.731][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-02-08 16:05:05.733][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-02-08 16:05:05.739][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-08 16:05:05.740][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-02-08 16:05:05.741][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-02-08 16:05:05.742][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:05.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:05.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:05.745][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-02-08 16:05:05.762][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-02-08 16:05:05.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:05.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:05.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:05.765][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-02-08 16:05:05.766][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-02-08 16:05:05.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:05.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:05.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:05.769][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-02-08 16:05:05.770][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-02-08 16:05:05.771][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-02-08 16:05:05.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:05.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:05.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:05.775][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-02-08 16:05:05.776][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-02-08 16:05:05.777][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-02-08 16:05:05.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:05.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:05.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:05.780][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-02-08 16:05:05.781][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-02-08 16:05:05.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:05.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:05.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:05.784][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-02-08 16:05:05.785][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-02-08 16:05:05.786][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-02-08 16:05:05.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:05.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:05.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:05.789][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-02-08 16:05:05.790][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-02-08 16:05:05.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:05.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:05.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:05.794][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-02-08 16:05:05.795][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-02-08 16:05:05.796][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-02-08 16:05:05.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:05.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:05.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:05.799][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-02-08 16:05:05.800][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-02-08 16:05:05.801][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-02-08 16:05:05.802][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-02-08 16:05:05.803][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-02-08 16:05:05.804][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-02-08 16:05:05.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:05.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:05.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:05.807][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-02-08 16:05:05.808][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-02-08 16:05:05.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:05.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:05.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:05.811][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-02-08 16:05:05.812][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-02-08 16:05:05.813][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:05.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:05.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:05.815][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-02-08 16:05:05.816][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-02-08 16:05:05.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:05.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:05.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:05.820][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-02-08 16:05:05.821][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-02-08 16:05:05.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:05.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:05.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:05.824][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-02-08 16:05:05.825][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-02-08 16:05:05.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:05.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:05.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:05.828][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-02-08 16:05:05.829][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-02-08 16:05:05.833][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-02-08 16:05:05.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:05.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:05.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:05.836][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-02-08 16:05:05.837][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-02-08 16:05:05.838][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-02-08 16:05:05.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:05.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:05.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:05.844][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-02-08 16:05:05.874][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:05.894][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-02-08 16:05:05.895][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:05.896][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-08 16:05:05.897][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:05.898][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-08 16:05:05.899][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:05.899][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-08 16:05:05.900][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-08 16:05:05.901][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-08 16:05:05.902][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:05.903][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-02-08 16:05:05.904][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-08 16:05:05.905][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:05.906][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:05.907][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-08 16:05:05.907][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-08 16:05:05.907][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-08 16:05:05.907][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-08 16:05:05.907][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-08 16:05:05.908][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-08 16:05:05.909][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:05:05.909][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:05:05.910][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-08 16:05:05.911][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:05:05.912][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:05:05.913][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-08 16:05:05.914][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:05.915][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-08 16:05:05.916][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-08 16:05:05.916][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:05.917][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:05.918][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-02-08 16:05:05.920][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:05.921][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-02-08 16:05:05.922][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:05.923][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-08 16:05:05.924][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:05.925][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-08 16:05:05.926][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:05.926][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-08 16:05:05.927][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-08 16:05:05.928][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-08 16:05:05.929][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:05.930][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-02-08 16:05:05.931][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-08 16:05:05.932][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:05.933][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:05.934][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-08 16:05:05.934][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-08 16:05:05.934][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-08 16:05:05.934][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-08 16:05:05.934][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-08 16:05:05.935][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-08 16:05:05.936][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:05:05.937][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:05:05.937][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-08 16:05:05.938][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:05:05.939][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:05:05.940][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-08 16:05:05.941][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:05.942][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-08 16:05:05.943][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-08 16:05:05.943][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:05.944][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:05.945][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-02-08 16:05:05.947][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:05.948][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-02-08 16:05:05.949][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:05.950][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-08 16:05:05.951][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:05.952][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-08 16:05:05.953][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:05.954][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-08 16:05:05.954][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-08 16:05:05.955][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-08 16:05:05.956][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:05.957][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-02-08 16:05:05.958][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-08 16:05:05.959][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:05.960][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:05.961][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:05.962][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-08 16:05:05.963][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:05:05.964][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:05:05.964][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-08 16:05:05.965][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:05:05.966][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:05:05.967][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-08 16:05:05.968][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:05.969][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-08 16:05:05.970][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-08 16:05:05.971][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:05.971][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:05.973][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-02-08 16:05:05.974][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:05.975][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-02-08 16:05:05.976][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:05.977][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-08 16:05:05.978][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:05.979][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-08 16:05:05.980][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:05.981][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-08 16:05:05.981][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-08 16:05:05.982][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-08 16:05:05.983][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:05.984][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-02-08 16:05:05.985][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-08 16:05:05.986][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:05.987][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:05.988][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:05.989][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-08 16:05:05.990][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:05:05.991][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:05:05.991][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-08 16:05:05.992][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:05:05.993][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:05:05.994][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-08 16:05:05.995][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:05.996][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-08 16:05:05.997][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-08 16:05:05.998][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:05.998][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:06.002][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-08 16:05:06.003][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.012][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[2025-02-08 16:05:06.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.088][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-02-08 16:05:06.094][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-02-08 16:05:06.096][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-02-08 16:05:06.097][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-02-08 16:05:06.099][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-08 16:05:06.100][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-08 16:05:06.101][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-02-08 16:05:06.103][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-02-08 16:05:06.104][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-02-08 16:05:06.106][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-08 16:05:06.107][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-08 16:05:06.109][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-02-08 16:05:06.110][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-02-08 16:05:06.111][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-02-08 16:05:06.113][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-02-08 16:05:06.114][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-08 16:05:06.116][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-02-08 16:05:06.117][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-02-08 16:05:06.119][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-08 16:05:06.120][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-02-08 16:05:06.122][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-02-08 16:05:06.123][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-02-08 16:05:06.125][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-02-08 16:05:06.126][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-02-08 16:05:06.127][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-02-08 16:05:06.129][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-02-08 16:05:06.130][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-02-08 16:05:06.132][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-02-08 16:05:06.133][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-02-08 16:05:06.135][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-02-08 16:05:06.136][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-02-08 16:05:06.138][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-02-08 16:05:06.139][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-02-08 16:05:06.141][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-02-08 16:05:06.142][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-02-08 16:05:06.144][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-02-08 16:05:06.145][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-02-08 16:05:06.146][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-02-08 16:05:06.148][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-02-08 16:05:06.149][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-02-08 16:05:06.151][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-02-08 16:05:06.152][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-02-08 16:05:06.154][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-02-08 16:05:06.155][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-02-08 16:05:06.157][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-02-08 16:05:06.158][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-02-08 16:05:06.160][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-02-08 16:05:06.161][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-02-08 16:05:06.162][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-02-08 16:05:06.164][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-02-08 16:05:06.165][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-02-08 16:05:06.167][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-02-08 16:05:06.168][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-02-08 16:05:06.170][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-02-08 16:05:06.171][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-02-08 16:05:06.173][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-02-08 16:05:06.174][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-02-08 16:05:06.175][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-02-08 16:05:06.177][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-02-08 16:05:06.178][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-02-08 16:05:06.180][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-02-08 16:05:06.181][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-02-08 16:05:06.183][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-02-08 16:05:06.184][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-02-08 16:05:06.186][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-02-08 16:05:06.187][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-02-08 16:05:06.188][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-08 16:05:06.190][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-08 16:05:06.191][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-02-08 16:05:06.193][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-02-08 16:05:06.194][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-02-08 16:05:06.196][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-02-08 16:05:06.197][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-02-08 16:05:06.198][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-02-08 16:05:06.200][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-02-08 16:05:06.201][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-02-08 16:05:06.203][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-02-08 16:05:06.204][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-02-08 16:05:06.206][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-02-08 16:05:06.207][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-02-08 16:05:06.208][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-02-08 16:05:06.210][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-02-08 16:05:06.211][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-02-08 16:05:06.218][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-02-08 16:05:06.220][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-02-08 16:05:06.223][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-08 16:05:06.224][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.226][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:06.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:06.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:06.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:06.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:06.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:06.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.261][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.DEBUG[2025-02-08 16:05:06.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:06.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:06.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:06.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:06.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:06.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:06.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:06.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:06.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:06.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:06.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:06.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:06.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:06.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:06.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:06.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:06.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:06.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:06.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:06.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:06.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:06.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:06.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:06.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:06.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:06.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:06.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:06.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:06.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:06.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:06.344][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-02-08 16:05:06.353][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-02-08 16:05:06.355][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:06.356][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-02-08 16:05:06.357][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:06.357][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-08 16:05:06.358][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:06.359][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-02-08 16:05:06.360][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:06.361][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-08 16:05:06.362][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-02-08 16:05:06.363][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-08 16:05:06.364][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:06.365][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-02-08 16:05:06.366][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-08 16:05:06.367][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-02-08 16:05:06.367][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-02-08 16:05:06.367][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-02-08 16:05:06.367][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-02-08 16:05:06.367][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-02-08 16:05:06.367][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-02-08 16:05:06.367][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-02-08 16:05:06.368][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:06.369][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:06.370][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-02-08 16:05:06.371][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:05:06.372][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:05:06.372][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-08 16:05:06.373][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:05:06.374][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:05:06.375][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-08 16:05:06.376][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-02-08 16:05:06.376][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-02-08 16:05:06.376][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-02-08 16:05:06.376][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-02-08 16:05:06.377][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-08 16:05:06.378][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-08 16:05:06.379][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:06.380][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:06.385][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-02-08 16:05:06.407][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-02-08 16:05:06.408][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-02-08 16:05:06.411][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-02-08 16:05:06.415][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-02-08 16:05:06.419][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-08 16:05:06.420][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-08 16:05:06.421][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-02-08 16:05:06.422][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-02-08 16:05:06.423][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-02-08 16:05:06.424][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-02-08 16:05:06.461][biodb::testThat]
biodb.INFO [2025-02-08 16:05:06.462][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-02-08 16:05:06.463][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-08 16:05:06.464][biodb::testThat]
biodb.TRACE[2025-02-08 16:05:06.467][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-02-08 16:05:06.469][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-02-08 16:05:06.472][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-02-08 16:05:06.479][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-08 16:05:06.479][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:06.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:06.491][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.493][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.494][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.TRACE[2025-02-08 16:05:06.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:06.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:06.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:06.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:06.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.529][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:06.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:06.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.556][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:06.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:06.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.560][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:06.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:06.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.564][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:06.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:06.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.568][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:06.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:06.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.572][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:06.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:06.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.576][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:06.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:06.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.580][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:06.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:06.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.584][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:06.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:06.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.588][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:06.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:06.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:06.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:06.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.596][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:06.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:06.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:06.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:06.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:06.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:06.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:06.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:06.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:06.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:06.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:06.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:06.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:06.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:06.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-08 16:05:06.658][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-02-08 16:05:06.660][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-08 16:05:06.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-08 16:05:06.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.664][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-08 16:05:06.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-08 16:05:06.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.667][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-02-08 16:05:06.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-02-08 16:05:06.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.671][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-02-08 16:05:06.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-02-08 16:05:06.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:06.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:06.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.703][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:06.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:06.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.710][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:06.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:06.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:06.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:06.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:06.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:06.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:06.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:06.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:06.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:06.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:06.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:06.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.733][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:06.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:06.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.737][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:06.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:06.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.741][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:06.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:06.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:06.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:06.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:06.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:06.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:06.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:06.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.765][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:06.766][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:06.767][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.768][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:06.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:06.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.779][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:06.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:06.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.783][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:06.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:06.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.787][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:06.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:06.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.790][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:06.791][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:06.792][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.793][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.794][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:06.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:06.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.804][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:06.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:06.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.808][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:06.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:06.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.811][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:06.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:06.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.815][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:06.816][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:06.817][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.818][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.819][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:06.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:06.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.829][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:06.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:06.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.833][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:06.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:06.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.836][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:06.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:06.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.840][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:06.841][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:06.842][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.843][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.844][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:06.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:06.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.854][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:06.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:06.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.858][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:06.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:06.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.861][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:06.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:06.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.865][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:06.866][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:06.867][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.868][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.869][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:06.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:06.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.879][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:06.880][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:06.880][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.881][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.889][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:06.890][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:06.891][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.892][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.895][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:06.896][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:06.897][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.898][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.902][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:06.903][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:06.904][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.905][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.908][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:06.909][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:06.910][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.911][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.926][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-02-08 16:05:06.959][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-02-08 16:05:06.960][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-02-08 16:05:06.962][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-08 16:05:06.962][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:06.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:06.967][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:06.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:06.969][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:06.970][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.TRACE[2025-02-08 16:05:06.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:06.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:06.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:06.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:06.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:06.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:06.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.002][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-08 16:05:07.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-08 16:05:07.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.009][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-08 16:05:07.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-08 16:05:07.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.014][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:07.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:07.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.017][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:07.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:07.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.021][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:07.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:07.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.025][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:07.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:07.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.029][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:07.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:07.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.033][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:07.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:07.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.036][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:07.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:07.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.040][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:07.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:07.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.044][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:07.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:07.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.048][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:07.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:07.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.051][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:07.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:07.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.056][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:07.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:07.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.060][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:07.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:07.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.065][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:07.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:07.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.069][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:07.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:07.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.073][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:07.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:07.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.077][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:07.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:07.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.084][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:07.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:07.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-08 16:05:07.111][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-02-08 16:05:07.131][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-08 16:05:07.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-08 16:05:07.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.135][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-08 16:05:07.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-08 16:05:07.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.138][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-02-08 16:05:07.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-02-08 16:05:07.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.145][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-02-08 16:05:07.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-02-08 16:05:07.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.157][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:07.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:07.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.187][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:07.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:07.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.191][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:07.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:07.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.195][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:07.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:07.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.224][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.225][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.226][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.227][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.238][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-08 16:05:07.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-08 16:05:07.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.242][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-08 16:05:07.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-08 16:05:07.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.245][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-08 16:05:07.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-08 16:05:07.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.249][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-08 16:05:07.250][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-08 16:05:07.251][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.252][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.253][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-08 16:05:07.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-08 16:05:07.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.263][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:07.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:07.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.266][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:07.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:07.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.270][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:07.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:07.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.274][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:07.278][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:07.279][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.280][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.281][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:07.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:07.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.291][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:07.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:07.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.295][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:07.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:07.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.298][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:07.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:07.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.302][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:07.303][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:07.304][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.305][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.306][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:07.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:07.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.316][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:07.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:07.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.319][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:07.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:07.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:07.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:07.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.327][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:07.328][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:07.328][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.329][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.330][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:07.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:07.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.341][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:07.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:07.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.345][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:07.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:07.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.348][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:07.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:07.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.352][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:07.353][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:07.354][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.355][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.356][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:07.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:07.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.365][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:07.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:07.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.369][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:07.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:07.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.373][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:07.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:07.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.377][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:07.378][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:07.378][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.379][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.380][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:07.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:07.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.390][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.391][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.392][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.393][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.397][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-08 16:05:07.398][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-08 16:05:07.399][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.400][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.403][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:07.404][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:07.405][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.406][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.413][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:07.414][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:07.415][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.416][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.420][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:07.421][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:07.422][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.423][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.426][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:07.427][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:07.428][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.429][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.433][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:07.434][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:07.435][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.435][ef$get] fields variable is a list.
biodb.INFO [2025-02-08 16:05:07.442][biodb::testThat]
biodb.INFO [2025-02-08 16:05:07.443][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-02-08 16:05:07.443][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-08 16:05:07.444][biodb::testThat]
biodb.DEBUG[2025-02-08 16:05:07.446][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-02-08 16:05:07.453][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2025-02-08 16:05:07.457][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.DEBUG[2025-02-08 16:05:07.458][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.TRACE[2025-02-08 16:05:07.460][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2025-02-08 16:05:07.461][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2025-02-08 16:05:07.463][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf".
biodb.DEBUG[2025-02-08 16:05:07.464][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2025-02-08 16:05:07.465][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2025-02-08 16:05:07.466][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2025-02-08 16:05:07.468][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-08 16:05:07.468][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:07.469][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:07.473][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:07.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:07.475][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:07.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-08 16:05:07.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.491][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:07.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:07.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.495][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:07.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:07.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.499][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:07.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:07.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.502][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:07.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:07.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.507][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:07.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:07.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.510][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:07.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:07.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.515][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:07.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:07.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.518][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:07.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:07.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.522][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:07.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:07.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.526][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:07.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:07.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.534][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:07.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:07.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-08 16:05:07.549][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-08 16:05:07.549][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:07.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:07.559][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:07.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:07.561][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:07.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-02-08 16:05:07.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.578][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-08 16:05:07.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-08 16:05:07.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.582][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-08 16:05:07.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-08 16:05:07.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.586][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:07.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:07.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.590][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:07.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:07.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.594][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:07.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:07.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.598][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:07.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:07.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.602][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:07.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:07.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.605][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:07.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:07.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.609][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:07.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:07.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.613][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:07.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:07.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.617][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:07.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:07.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.620][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:07.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:07.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.624][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:07.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:07.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.629][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:07.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:07.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.632][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:07.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:07.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.637][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:07.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:07.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.640][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:07.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:07.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.645][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:07.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:07.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.648][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:07.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:07.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.656][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:07.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:07.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:07.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:07.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-08 16:05:07.697][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2025-02-08 16:05:07.698][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-02-08 16:05:07.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-02-08 16:05:07.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-02-08 16:05:07.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-02-08 16:05:07.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.705][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-02-08 16:05:07.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-02-08 16:05:07.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.712][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-02-08 16:05:07.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-02-08 16:05:07.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.716][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-02-08 16:05:07.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-02-08 16:05:07.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.720][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-02-08 16:05:07.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-02-08 16:05:07.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-08 16:05:07.729][biodb::testThat]
biodb.INFO [2025-02-08 16:05:07.730][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-02-08 16:05:07.731][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-08 16:05:07.732][biodb::testThat]
biodb.INFO [2025-02-08 16:05:07.737][biodb::testThat]
biodb.INFO [2025-02-08 16:05:07.738][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-02-08 16:05:07.739][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-08 16:05:07.740][biodb::testThat]
biodb.WARN [2025-02-08 16:05:07.758][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-02-08 16:05:07.776][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-02-08 16:05:07.783][biodb::testThat]
biodb.INFO [2025-02-08 16:05:07.784][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-02-08 16:05:07.785][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-08 16:05:07.786][biodb::testThat]
biodb.TRACE[2025-02-08 16:05:07.807][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-08 16:05:07.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-08 16:05:07.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.811][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-08 16:05:07.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-08 16:05:07.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.819][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-02-08 16:05:07.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-02-08 16:05:07.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.823][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-02-08 16:05:07.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-02-08 16:05:07.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.858][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-08 16:05:07.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-08 16:05:07.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.862][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-08 16:05:07.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-08 16:05:07.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.865][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-02-08 16:05:07.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-02-08 16:05:07.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:07.869][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-02-08 16:05:07.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-02-08 16:05:07.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:07.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-08 16:05:07.877][biodb::testThat]
biodb.INFO [2025-02-08 16:05:07.878][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-02-08 16:05:07.879][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-08 16:05:07.880][biodb::testThat]
biodb.INFO [2025-02-08 16:05:07.887][biodb::testThat]
biodb.INFO [2025-02-08 16:05:07.888][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-02-08 16:05:07.889][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-08 16:05:07.889][biodb::testThat]
biodb.INFO [2025-02-08 16:05:07.896][biodb::testThat]
biodb.INFO [2025-02-08 16:05:07.897][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-02-08 16:05:07.898][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-08 16:05:07.898][biodb::testThat]
biodb.INFO [2025-02-08 16:05:07.904][biodb::testThat]
biodb.INFO [2025-02-08 16:05:07.905][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-02-08 16:05:07.906][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-08 16:05:07.906][biodb::testThat]
biodb.INFO [2025-02-08 16:05:07.912][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-02-08 16:05:07.913][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-02-08 16:05:07.914][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-02-08 16:05:07.915][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-02-08 16:05:07.915][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:07.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:07.917][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:07.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:07.919][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:07.920][FUN] Functions in observer BiodbConfig: [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 [2025-02-08 16:05:07.928][biodb::testContext]
biodb.INFO [2025-02-08 16:05:07.929][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-08 16:05:07.930][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-02-08 16:05:07.931][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-08 16:05:07.932][biodb::testContext]
biodb.INFO [2025-02-08 16:05:07.934][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-02-08 16:05:07.935][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2025-02-08 16:05:07.939][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-08 16:05:07.940][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-02-08 16:05:07.945][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-02-08 16:05:07.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:07.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:07.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:07.948][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-02-08 16:05:07.949][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-02-08 16:05:07.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:07.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:07.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:07.953][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-02-08 16:05:07.954][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-02-08 16:05:07.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:07.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:07.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:07.957][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-02-08 16:05:07.958][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-02-08 16:05:07.959][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-02-08 16:05:07.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:07.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:07.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:07.962][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-02-08 16:05:07.963][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-02-08 16:05:07.964][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-02-08 16:05:07.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:07.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:07.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:07.967][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-02-08 16:05:07.968][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-02-08 16:05:07.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:07.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:07.971][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[2025-02-08 16:05:07.972][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-02-08 16:05:07.973][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-02-08 16:05:07.974][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-02-08 16:05:07.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:07.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:07.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:07.977][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-02-08 16:05:07.978][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-02-08 16:05:07.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:07.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:07.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:07.981][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-02-08 16:05:07.982][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-02-08 16:05:07.983][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-02-08 16:05:07.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:07.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:07.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:07.987][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-02-08 16:05:07.988][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-02-08 16:05:07.989][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-02-08 16:05:07.990][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-02-08 16:05:07.991][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-02-08 16:05:07.992][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-02-08 16:05:07.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:07.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:07.994][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[2025-02-08 16:05:07.995][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-02-08 16:05:07.996][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-02-08 16:05:07.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:07.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:07.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:07.999][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-02-08 16:05:08.000][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-02-08 16:05:08.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.003][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[2025-02-08 16:05:08.004][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-02-08 16:05:08.005][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-02-08 16:05:08.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.008][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-02-08 16:05:08.009][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-02-08 16:05:08.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.012][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-02-08 16:05:08.013][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-02-08 16:05:08.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.017][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-02-08 16:05:08.018][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-02-08 16:05:08.022][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-02-08 16:05:08.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.025][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-02-08 16:05:08.026][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-02-08 16:05:08.027][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-02-08 16:05:08.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.031][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-02-08 16:05:08.057][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:08.058][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-02-08 16:05:08.059][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:08.060][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-08 16:05:08.061][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:08.062][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-08 16:05:08.063][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:08.064][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-08 16:05:08.065][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-08 16:05:08.066][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-08 16:05:08.070][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:08.071][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-02-08 16:05:08.072][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-08 16:05:08.073][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:08.074][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:08.075][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-08 16:05:08.075][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-08 16:05:08.075][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-08 16:05:08.075][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-08 16:05:08.075][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-08 16:05:08.076][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-08 16:05:08.077][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:05:08.078][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:05:08.079][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-08 16:05:08.080][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:05:08.080][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:05:08.081][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-08 16:05:08.082][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:08.083][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-08 16:05:08.084][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-08 16:05:08.085][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:08.086][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:08.087][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-02-08 16:05:08.088][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:08.089][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-02-08 16:05:08.090][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:08.091][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-08 16:05:08.092][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:08.093][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-08 16:05:08.094][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:08.095][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-08 16:05:08.096][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-08 16:05:08.097][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-08 16:05:08.098][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:08.099][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-02-08 16:05:08.100][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-08 16:05:08.101][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:08.102][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:08.103][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-08 16:05:08.103][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-08 16:05:08.103][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-08 16:05:08.103][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-08 16:05:08.103][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-08 16:05:08.104][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-08 16:05:08.104][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:05:08.105][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:05:08.106][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-08 16:05:08.107][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:05:08.108][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:05:08.109][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-08 16:05:08.110][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:08.111][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-08 16:05:08.112][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-08 16:05:08.112][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:08.113][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:08.114][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-02-08 16:05:08.116][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:08.117][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-02-08 16:05:08.118][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:08.119][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-08 16:05:08.120][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:08.121][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-08 16:05:08.122][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:08.123][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-08 16:05:08.124][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-08 16:05:08.125][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-08 16:05:08.125][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:08.126][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-02-08 16:05:08.127][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-08 16:05:08.128][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:08.129][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:08.130][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:08.131][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-08 16:05:08.132][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:05:08.133][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:05:08.134][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-08 16:05:08.135][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:05:08.135][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:05:08.136][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-08 16:05:08.137][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:08.138][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-08 16:05:08.139][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-08 16:05:08.140][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:08.141][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:08.142][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-02-08 16:05:08.143][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:08.144][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-02-08 16:05:08.145][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:08.146][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-08 16:05:08.147][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:08.148][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-08 16:05:08.149][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:08.150][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-08 16:05:08.151][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-08 16:05:08.152][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-08 16:05:08.153][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:08.154][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-02-08 16:05:08.155][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-08 16:05:08.156][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:08.156][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:08.157][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:08.158][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-08 16:05:08.159][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:05:08.160][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:05:08.161][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-08 16:05:08.162][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:05:08.163][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:05:08.164][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-08 16:05:08.164][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:08.165][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-08 16:05:08.166][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-08 16:05:08.167][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:08.168][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:08.169][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-08 16:05:08.170][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.179][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.214][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.228][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[2025-02-08 16:05:08.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.246][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-02-08 16:05:08.247][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-02-08 16:05:08.248][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-02-08 16:05:08.250][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-02-08 16:05:08.251][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-08 16:05:08.252][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-08 16:05:08.254][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-02-08 16:05:08.255][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-02-08 16:05:08.256][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-02-08 16:05:08.257][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-08 16:05:08.259][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-08 16:05:08.260][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-02-08 16:05:08.261][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-02-08 16:05:08.263][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-02-08 16:05:08.264][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-02-08 16:05:08.265][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-08 16:05:08.266][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-02-08 16:05:08.268][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-02-08 16:05:08.269][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-08 16:05:08.270][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-02-08 16:05:08.272][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-02-08 16:05:08.273][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-02-08 16:05:08.274][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-02-08 16:05:08.276][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-02-08 16:05:08.277][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-02-08 16:05:08.278][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-02-08 16:05:08.279][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-02-08 16:05:08.281][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-02-08 16:05:08.282][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-02-08 16:05:08.283][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-02-08 16:05:08.285][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-02-08 16:05:08.286][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-02-08 16:05:08.287][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-02-08 16:05:08.289][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-02-08 16:05:08.290][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-02-08 16:05:08.291][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-02-08 16:05:08.292][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-02-08 16:05:08.294][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-02-08 16:05:08.295][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-02-08 16:05:08.296][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-02-08 16:05:08.298][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-02-08 16:05:08.299][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-02-08 16:05:08.300][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-02-08 16:05:08.301][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-02-08 16:05:08.303][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-02-08 16:05:08.304][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-02-08 16:05:08.305][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-02-08 16:05:08.307][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-02-08 16:05:08.308][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-02-08 16:05:08.309][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-02-08 16:05:08.310][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-02-08 16:05:08.312][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-02-08 16:05:08.313][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-02-08 16:05:08.314][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-02-08 16:05:08.316][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-02-08 16:05:08.317][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-02-08 16:05:08.318][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-02-08 16:05:08.320][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-02-08 16:05:08.321][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-02-08 16:05:08.326][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-02-08 16:05:08.327][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-02-08 16:05:08.328][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-02-08 16:05:08.330][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-02-08 16:05:08.331][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-02-08 16:05:08.332][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-02-08 16:05:08.334][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-02-08 16:05:08.335][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-08 16:05:08.336][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-08 16:05:08.337][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-02-08 16:05:08.339][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-02-08 16:05:08.340][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-02-08 16:05:08.341][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-02-08 16:05:08.342][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-02-08 16:05:08.344][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-02-08 16:05:08.345][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-02-08 16:05:08.346][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-02-08 16:05:08.348][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-02-08 16:05:08.349][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-02-08 16:05:08.350][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-02-08 16:05:08.351][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-02-08 16:05:08.353][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-02-08 16:05:08.354][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-02-08 16:05:08.355][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-02-08 16:05:08.357][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-02-08 16:05:08.358][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-02-08 16:05:08.359][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-08 16:05:08.360][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.362][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:08.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:08.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:08.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:08.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.374][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[2025-02-08 16:05:08.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:08.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:08.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.380][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[2025-02-08 16:05:08.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:08.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:08.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:08.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:08.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:08.394][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:08.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:08.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:08.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:08.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:08.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:08.411][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:08.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:08.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:08.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:08.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:08.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:08.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:08.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:08.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:08.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:08.440][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:08.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:08.446][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:08.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:08.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:08.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:08.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:08.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:08.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:08.466][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-02-08 16:05:08.475][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-02-08 16:05:08.477][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:08.478][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-02-08 16:05:08.479][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:08.480][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-08 16:05:08.481][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:08.482][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-02-08 16:05:08.483][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:08.484][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-08 16:05:08.485][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-02-08 16:05:08.486][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-08 16:05:08.487][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:08.487][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-02-08 16:05:08.488][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-08 16:05:08.489][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-02-08 16:05:08.489][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-02-08 16:05:08.489][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-02-08 16:05:08.489][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-02-08 16:05:08.489][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-02-08 16:05:08.489][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-02-08 16:05:08.489][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-02-08 16:05:08.490][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:08.491][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:08.492][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-02-08 16:05:08.493][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:05:08.494][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:05:08.495][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-08 16:05:08.496][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:05:08.497][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:05:08.498][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-08 16:05:08.498][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-02-08 16:05:08.498][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-02-08 16:05:08.498][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-02-08 16:05:08.498][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-02-08 16:05:08.499][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-08 16:05:08.500][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-08 16:05:08.501][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:08.502][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:08.503][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-02-08 16:05:08.506][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-02-08 16:05:08.507][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-02-08 16:05:08.508][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-02-08 16:05:08.510][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-02-08 16:05:08.511][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-08 16:05:08.512][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-08 16:05:08.513][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-02-08 16:05:08.514][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-02-08 16:05:08.515][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-02-08 16:05:08.516][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-02-08 16:05:08.517][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-02-08 16:05:08.518][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-02-08 16:05:08.519][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-02-08 16:05:08.520][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-02-08 16:05:08.521][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:08.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:08.522][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:08.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:08.524][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:08.525][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ]
> 
> proc.time()
   user  system elapsed 
  4.279   0.218   4.488

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.11.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NciCactusConn.Rd: BiodbConn
  NciCactusEntry.Rd: BiodbSdfEntry
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/00check.log’
for details.

Installation output

biodbNci.Rcheck/00install.out

* installing *source* package ‘biodbNci’ ...
** this is package ‘biodbNci’ version ‘1.11.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c extractEntries.cpp -o extractEntries.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c test-100-example.cpp -o test-100-example.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/testthat/include' -I/usr/local/include    -fpic  -g -O2  -DR_NO_REMAP -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-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)