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 palomino7

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: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --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 16:04:40 -0500 (Sat, 08 Feb 2025)
EndedAt: 2025-02-08 17:01:14 -0500 (Sat, 08 Feb 2025)
EllapsedTime: 3393.9 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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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 16:05:54.694][biodb::testContext]
biodb.INFO [2025-02-08 16:05:54.697][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-08 16:05:54.698][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-02-08 16:05:54.699][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-08 16:05:54.700][biodb::testContext]
biodb.INFO [2025-02-08 16:05:54.706][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-02-08 16:05:54.709][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-02-08 16:05:54.717][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-08 16:05:54.718][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-02-08 16:05:54.719][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-02-08 16:05:54.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:54.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:54.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:54.723][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-02-08 16:05:54.739][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-02-08 16:05:54.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:54.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:54.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:54.743][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-02-08 16:05:54.745][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-02-08 16:05:54.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:54.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:54.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:54.749][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-02-08 16:05:54.750][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-02-08 16:05:54.751][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-02-08 16:05:54.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:54.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:54.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:54.755][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-02-08 16:05:54.757][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-02-08 16:05:54.758][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-02-08 16:05:54.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:54.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:54.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:54.762][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-02-08 16:05:54.763][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-02-08 16:05:54.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:54.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:54.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:54.767][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-02-08 16:05:54.768][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-02-08 16:05:54.770][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-02-08 16:05:54.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:54.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:54.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:54.774][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-02-08 16:05:54.775][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-02-08 16:05:54.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:54.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:54.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:54.779][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-02-08 16:05:54.780][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-02-08 16:05:54.781][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-02-08 16:05:54.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:54.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:54.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:54.786][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-02-08 16:05:54.787][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-02-08 16:05:54.788][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-02-08 16:05:54.789][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-02-08 16:05:54.790][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-02-08 16:05:54.791][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-02-08 16:05:54.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:54.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:54.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:54.796][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-02-08 16:05:54.797][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-02-08 16:05:54.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:54.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:54.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:54.801][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-02-08 16:05:54.802][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-02-08 16:05:54.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:54.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:54.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:54.806][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-02-08 16:05:54.808][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-02-08 16:05:54.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:54.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:54.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:54.812][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-02-08 16:05:54.813][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-02-08 16:05:54.814][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:54.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:54.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:54.817][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-02-08 16:05:54.818][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-02-08 16:05:54.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:54.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:54.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:54.823][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-02-08 16:05:54.824][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-02-08 16:05:54.827][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-02-08 16:05:54.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:54.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:54.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:54.831][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-02-08 16:05:54.832][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-02-08 16:05:54.834][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-02-08 16:05:54.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:54.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:54.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:54.840][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-02-08 16:05:54.867][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:54.887][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-02-08 16:05:54.888][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:54.889][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-08 16:05:54.890][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:54.892][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-08 16:05:54.893][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:54.894][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-08 16:05:54.895][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-08 16:05:54.896][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-08 16:05:54.897][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:54.899][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-02-08 16:05:54.900][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-08 16:05:54.901][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:54.902][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:54.903][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-08 16:05:54.903][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-08 16:05:54.903][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-08 16:05:54.903][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-08 16:05:54.903][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-08 16:05:54.905][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-08 16:05:54.906][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:05:54.907][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:05:54.908][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-08 16:05:54.909][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:05:54.910][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:05:54.911][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-08 16:05:54.912][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:54.913][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-08 16:05:54.914][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-08 16:05:54.916][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:54.917][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:54.918][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-02-08 16:05:54.920][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:54.921][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-02-08 16:05:54.922][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:54.923][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-08 16:05:54.925][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:54.926][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-08 16:05:54.927][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:54.928][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-08 16:05:54.929][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-08 16:05:54.930][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-08 16:05:54.932][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:54.933][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-02-08 16:05:54.934][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-08 16:05:54.935][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:54.936][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:54.937][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-08 16:05:54.937][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-08 16:05:54.937][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-08 16:05:54.937][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-08 16:05:54.937][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-08 16:05:54.939][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-08 16:05:54.940][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:05:54.941][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:05:54.942][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-08 16:05:54.943][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:05:54.944][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:05:54.945][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-08 16:05:54.946][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:54.947][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-08 16:05:54.948][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-08 16:05:54.950][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:54.951][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:54.952][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-02-08 16:05:54.954][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:54.955][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-02-08 16:05:54.956][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:54.957][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-08 16:05:54.959][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:54.960][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-08 16:05:54.961][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:54.962][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-08 16:05:54.963][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-08 16:05:54.964][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-08 16:05:54.965][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:54.967][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-02-08 16:05:54.968][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-08 16:05:54.969][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:54.970][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:54.971][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:54.972][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-08 16:05:54.973][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:05:54.975][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:05:54.976][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-08 16:05:54.977][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:05:54.978][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:05:54.979][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-08 16:05:54.980][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:54.981][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-08 16:05:54.982][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-08 16:05:54.983][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:54.984][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:54.986][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-02-08 16:05:54.988][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:54.989][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-02-08 16:05:54.990][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:54.991][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-08 16:05:54.992][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:54.993][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-08 16:05:54.995][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:54.996][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-08 16:05:54.997][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-08 16:05:54.998][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-08 16:05:54.999][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:55.000][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-02-08 16:05:55.002][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-08 16:05:55.003][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:55.004][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:55.005][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:55.006][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-08 16:05:55.007][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:05:55.008][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:05:55.010][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-08 16:05:55.011][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:05:55.012][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:05:55.013][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-08 16:05:55.014][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:55.015][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-08 16:05:55.016][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-08 16:05:55.017][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:55.019][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:55.022][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-08 16:05:55.023][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.024][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 16:05:55.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.027][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 16:05:55.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:55.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.033][FUN] 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 16:05:55.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:55.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.038][FUN] 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 16:05:55.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:55.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.043][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 16:05:55.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.045][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 16:05:55.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.049][FUN] 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 16:05:55.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:55.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.054][FUN] 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 16:05:55.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:55.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.059][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 16:05:55.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.061][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 16:05:55.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.064][FUN] 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 16:05:55.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:55.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.070][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 16:05:55.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.072][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 16:05:55.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.075][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 16:05:55.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.077][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 16:05:55.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.080][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 16:05:55.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.082][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 16:05:55.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.086][FUN] 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 16:05:55.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:55.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:55.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:55.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:55.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:55.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:55.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:55.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.111][FUN] 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 16:05:55.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:55.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.117][FUN] 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 16:05:55.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:55.120][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-02-08 16:05:55.124][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-02-08 16:05:55.125][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-02-08 16:05:55.127][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-02-08 16:05:55.129][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-08 16:05:55.130][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-08 16:05:55.132][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-02-08 16:05:55.133][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-02-08 16:05:55.135][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-02-08 16:05:55.136][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-08 16:05:55.138][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-08 16:05:55.139][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-02-08 16:05:55.141][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-02-08 16:05:55.142][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-02-08 16:05:55.144][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-02-08 16:05:55.145][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-08 16:05:55.147][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-02-08 16:05:55.148][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-02-08 16:05:55.150][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-08 16:05:55.151][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-02-08 16:05:55.153][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-02-08 16:05:55.154][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-02-08 16:05:55.156][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-02-08 16:05:55.157][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-02-08 16:05:55.159][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-02-08 16:05:55.160][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-02-08 16:05:55.162][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-02-08 16:05:55.163][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-02-08 16:05:55.165][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-02-08 16:05:55.166][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-02-08 16:05:55.168][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-02-08 16:05:55.169][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-02-08 16:05:55.171][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-02-08 16:05:55.172][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-02-08 16:05:55.174][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-02-08 16:05:55.175][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-02-08 16:05:55.177][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-02-08 16:05:55.178][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-02-08 16:05:55.180][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-02-08 16:05:55.181][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-02-08 16:05:55.183][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-02-08 16:05:55.184][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-02-08 16:05:55.186][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-02-08 16:05:55.187][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-02-08 16:05:55.189][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-02-08 16:05:55.190][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-02-08 16:05:55.192][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-02-08 16:05:55.193][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-02-08 16:05:55.195][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-02-08 16:05:55.196][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-02-08 16:05:55.198][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-02-08 16:05:55.199][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-02-08 16:05:55.201][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-02-08 16:05:55.202][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-02-08 16:05:55.204][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-02-08 16:05:55.205][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-02-08 16:05:55.207][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-02-08 16:05:55.208][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-02-08 16:05:55.210][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-02-08 16:05:55.211][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-02-08 16:05:55.213][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-02-08 16:05:55.214][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-02-08 16:05:55.216][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-02-08 16:05:55.217][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-02-08 16:05:55.219][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-02-08 16:05:55.220][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-02-08 16:05:55.222][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-08 16:05:55.223][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-08 16:05:55.225][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-02-08 16:05:55.226][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-02-08 16:05:55.228][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-02-08 16:05:55.229][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-02-08 16:05:55.231][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-02-08 16:05:55.232][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-02-08 16:05:55.234][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-02-08 16:05:55.235][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-02-08 16:05:55.237][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-02-08 16:05:55.238][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-02-08 16:05:55.240][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-02-08 16:05:55.241][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-02-08 16:05:55.243][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-02-08 16:05:55.244][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-02-08 16:05:55.246][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-02-08 16:05:55.268][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-02-08 16:05:55.271][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-02-08 16:05:55.274][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-08 16:05:55.275][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.276][FUN] 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 16:05:55.277][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.278][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 16:05:55.282][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:55.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:55.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:55.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:55.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:55.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:55.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.294][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 16:05:55.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.296][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 16:05:55.297][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:55.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:55.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.301][FUN] 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 16:05:55.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:55.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:55.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:55.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:55.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:55.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:55.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:55.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:55.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:55.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:55.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:55.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.350][FUN] 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 16:05:55.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:55.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:55.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:55.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.357][FUN] 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 16:05:55.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:55.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:55.362][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:55.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.364][FUN] 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 16:05:55.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:55.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:55.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:55.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.372][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 16:05:55.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.374][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 16:05:55.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:55.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:55.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.379][FUN] 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 16:05:55.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:55.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:55.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:55.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:55.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:55.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:55.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:55.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:55.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:55.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:55.399][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:55.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.401][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 16:05:55.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.403][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 16:05:55.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:55.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:55.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 16:05:55.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 16:05:55.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:55.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:55.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.416][FUN] 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 16:05:55.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:55.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:55.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:55.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.423][FUN] 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 16:05:55.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:05:55.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 16:05:55.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:55.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:55.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.430][FUN] 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 16:05:55.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.432][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 16:05:55.435][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-02-08 16:05:55.444][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-02-08 16:05:55.446][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:55.447][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-02-08 16:05:55.448][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:55.449][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-08 16:05:55.451][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:55.452][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-02-08 16:05:55.453][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:55.454][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-08 16:05:55.455][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-02-08 16:05:55.456][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-08 16:05:55.458][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:55.459][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-02-08 16:05:55.460][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-08 16:05:55.461][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-02-08 16:05:55.461][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-02-08 16:05:55.461][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-02-08 16:05:55.461][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-02-08 16:05:55.461][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-02-08 16:05:55.461][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-02-08 16:05:55.461][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-02-08 16:05:55.462][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-02-08 16:05:55.463][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:55.465][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-02-08 16:05:55.466][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:05:55.467][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:05:55.468][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-08 16:05:55.469][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 16:05:55.470][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 16:05:55.471][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-08 16:05:55.472][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-02-08 16:05:55.472][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-02-08 16:05:55.472][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-02-08 16:05:55.472][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-02-08 16:05:55.473][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-08 16:05:55.474][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-08 16:05:55.476][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-02-08 16:05:55.477][self$setPropertyValue]
biodb.DEBUG[2025-02-08 16:05:55.482][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-02-08 16:05:55.502][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-02-08 16:05:55.504][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-02-08 16:05:55.508][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-02-08 16:05:55.511][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-02-08 16:05:55.515][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-08 16:05:55.516][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-08 16:05:55.518][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-02-08 16:05:55.519][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-02-08 16:05:55.521][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-02-08 16:05:55.522][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-02-08 16:05:55.531][biodb::testThat]
biodb.INFO [2025-02-08 16:05:55.532][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-02-08 16:05:55.534][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-08 16:05:55.535][biodb::testThat]
biodb.TRACE[2025-02-08 16:05:55.540][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2025-02-08 16:05:55.542][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-02-08 16:05:55.546][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-02-08 16:05:55.560][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-08 16:05:55.561][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:55.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:55.577][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:55.579][FUN] 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 16:05:55.580][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:55.581][FUN] Functions in observer BiodbConfig: [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 16:05:55.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:55.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:55.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:55.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:55.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.616][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:55.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:55.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.641][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:55.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:55.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.647][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:55.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:55.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.652][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:55.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:55.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.657][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:55.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:55.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.662][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:55.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:55.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.667][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:55.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:55.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.672][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:55.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:55.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.677][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:55.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:55.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.682][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:55.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:55.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:55.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:55.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.691][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:55.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:55.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:55.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:55.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:55.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:55.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:55.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:55.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:55.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:55.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:55.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:55.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:55.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:55.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-08 16:05:55.756][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-02-08 16:05:55.759][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-08 16:05:55.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-08 16:05:55.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.764][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-08 16:05:55.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-08 16:05:55.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.769][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-02-08 16:05:55.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-02-08 16:05:55.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.773][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-02-08 16:05:55.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-02-08 16:05:55.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:55.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:55.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.814][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:55.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:55.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:55.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:55.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:55.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:55.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:55.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:55.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:55.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:55.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:55.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:55.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:55.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:55.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.854][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:55.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:55.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.859][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:55.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:55.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.863][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:55.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:55.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:55.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:55.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:55.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:55.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:55.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:55.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.895][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:55.896][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:55.897][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.899][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:55.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:55.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.914][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:55.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:55.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.919][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:55.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:55.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.924][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:55.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:55.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.928][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:55.930][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:55.931][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.932][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.933][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:55.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:55.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.947][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:55.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:55.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.952][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:55.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:55.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:55.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:55.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.961][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:55.962][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:55.963][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.964][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.966][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:55.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:55.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.980][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:55.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:55.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.985][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:55.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:55.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.989][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:55.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:55.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.994][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:55.995][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:55.996][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:55.997][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:55.999][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:56.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:56.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.013][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:56.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:56.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.017][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:56.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:56.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.022][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:56.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:56.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.027][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:56.028][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:56.029][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.030][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.031][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:56.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:56.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.045][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:56.046][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:56.048][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.049][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.055][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:56.056][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:56.057][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.059][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.070][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:56.071][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:56.072][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.073][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.080][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:56.081][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:56.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.083][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.090][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:56.091][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:56.092][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.093][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.111][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2025-02-08 16:05:56.140][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-02-08 16:05:56.141][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-02-08 16:05:56.143][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-08 16:05:56.144][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 16:05:56.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 16:05:56.152][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 16:05:56.153][FUN] 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 16:05:56.154][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-08 16:05:56.155][FUN] Functions in observer BiodbConfig: [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 16:05:56.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:56.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:56.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:56.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:56.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.188][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-08 16:05:56.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-08 16:05:56.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.193][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-08 16:05:56.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-08 16:05:56.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.203][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:56.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:56.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.207][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:56.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:56.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.212][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:56.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:56.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.217][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:56.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:56.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.222][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:56.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:56.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.227][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:56.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:56.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.231][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:56.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:56.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.236][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:56.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:56.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.241][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:56.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:56.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.245][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:56.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:56.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.250][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:56.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:56.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.255][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:56.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:56.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.260][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:56.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:56.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.265][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:56.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:56.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.270][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:56.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:56.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.275][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:56.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:56.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.280][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:56.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:56.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:56.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:56.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.289][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:56.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:56.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:56.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:56.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:56.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:56.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:56.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:56.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:56.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:56.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:56.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:56.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:56.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:56.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-08 16:05:56.322][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-02-08 16:05:56.339][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-08 16:05:56.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-08 16:05:56.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.344][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-08 16:05:56.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-08 16:05:56.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.349][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-02-08 16:05:56.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-02-08 16:05:56.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.353][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-02-08 16:05:56.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-02-08 16:05:56.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:56.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:56.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.373][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:56.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:56.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:56.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:56.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:56.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:56.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:56.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:56.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:56.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:56.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:56.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:56.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:56.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:56.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.413][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:56.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:56.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.418][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:56.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:56.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.422][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:56.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 16:05:56.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:56.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:56.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:56.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:56.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:56.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:56.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.457][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:56.458][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:56.459][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.461][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:56.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:56.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.476][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-08 16:05:56.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-08 16:05:56.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.480][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-08 16:05:56.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-08 16:05:56.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.485][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-08 16:05:56.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-08 16:05:56.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.490][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-08 16:05:56.491][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-08 16:05:56.492][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.493][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.494][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-08 16:05:56.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-08 16:05:56.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.508][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:56.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:56.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.512][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:56.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:56.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.517][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:56.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:56.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.522][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:56.523][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:56.524][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.525][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.526][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:56.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:56.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.548][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:56.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:56.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.553][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:56.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:56.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.558][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:56.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:56.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.563][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:56.564][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:56.565][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.566][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.567][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:56.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:56.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.581][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:56.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:56.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.586][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:56.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:56.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.591][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:56.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:56.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.596][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:56.597][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:56.598][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.599][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.600][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:56.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:56.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.614][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:56.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:56.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.619][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:56.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:56.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.623][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:56.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:56.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.628][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:56.629][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:56.630][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.631][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.632][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:56.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:56.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.646][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:56.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:56.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.651][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:56.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:56.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.656][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:56.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:56.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.660][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:56.662][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:56.663][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.664][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.665][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:56.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:56.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.679][ef$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 16:05:56.681][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 16:05:56.682][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.683][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.690][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-08 16:05:56.691][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-08 16:05:56.692][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.693][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.699][ef$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 16:05:56.701][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 16:05:56.702][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.703][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.709][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 16:05:56.710][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 16:05:56.711][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.717][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.723][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 16:05:56.725][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 16:05:56.726][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.727][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.733][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:56.734][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 16:05:56.735][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.736][ef$get] fields variable is a list.
biodb.TRACE[2025-02-08 16:05:56.743][ef$get] Asked field names are: name.
biodb.TRACE[2025-02-08 16:05:56.744][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 16:05:56.745][ef$get] 1 fields were returned.
biodb.TRACE[2025-02-08 16:05:56.746][ef$get] fields variable is a list.
biodb.INFO [2025-02-08 16:05:56.758][biodb::testThat]
biodb.INFO [2025-02-08 16:05:56.759][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-02-08 16:05:56.760][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-08 16:05:56.761][biodb::testThat]
biodb.DEBUG[2025-02-08 16:05:56.764][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-02-08 16:05:56.770][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.INFO [2025-02-08 16:05:56.776][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427" for "nci.cactus-8efc65070d01b214e760b1d4932ee427".
biodb.DEBUG[2025-02-08 16:05:56.778][self$isDownloaded] Database nci.cactus has not yet been downloaded.
biodb.INFO [2025-02-08 16:05:56.779][self$download] Downloading whole database of nci.cactus.
biodb.INFO [2025-02-08 16:05:56.780][private$doDownload] Downloading NCI CACTUS database at "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz" ...
biodb.DEBUG[2025-02-08 16:05:56.782][sched$downloadFile] Downloading file "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
trying URL 'https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz'
Content type 'application/x-gzip' length 206737123 bytes (197.2 MB)
==================================================
downloaded 197.2 MB

biodb.TRACE[2025-02-08 16:06:33.080][cch$addFilesToCache] Moving files to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp\nci.cactus491c3bf03f9fgz".
biodb.TRACE[2025-02-08 16:06:33.082][private$doAddFilesToCache] Destination files are [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2025-02-08 16:06:33.088][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2025-02-08 16:06:33.090][self$getDownloadPath] Download path of nci.cactus is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2025-02-08 16:06:33.091][self$download] Downloading of nci.cactus completed.
biodb.TRACE[2025-02-08 16:06:33.094][self$addFilesToCache] Moving files to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp\marker491c1711150marker".
biodb.TRACE[2025-02-08 16:06:33.095][private$doAddFilesToCache] Destination files are [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/downloaded.marker".
biodb.DEBUG[2025-02-08 16:06:33.100][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-02-08 16:06:33.102][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-02-08 16:06:33.104][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-02-08 16:06:33.105][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.DEBUG[2025-02-08 16:06:33.107][self$getDownloadPath] Download path of nci.cactus is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2025-02-08 16:08:31.291][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2025-02-08 16:08:31.293][private$doExtractDownload] Extract single entries from downloaded file "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp/cactus_rdfs", into "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp".
biodb.TRACE[2025-02-08 16:39:30.730][self$addFilesToCache] Moving files to cache [265242]: "C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/entry_1.txt, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/entry_2.txt, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/entry_3.txt, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/entry_4.txt, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/entry_5.txt, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/entry_6.txt, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/entry_7.txt, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/entry_8.txt, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/entry_9.txt, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/entry_10.txt, ...".
biodb.TRACE[2025-02-08 16:39:31.444][private$doAddFilesToCache] Destination files are [265242]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/1.sdf, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/2.sdf, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/3.sdf, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/4.sdf, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/5.sdf, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/6.sdf, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/7.sdf, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/8.sdf, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/9.sdf, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/10.sdf, ...".
biodb.DEBUG[2025-02-08 17:01:10.255][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-02-08 17:01:10.338][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2025-02-08 17:01:10.428][self$addFilesToCache] Moving files to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp\marker491c6de14f0emarker".
biodb.TRACE[2025-02-08 17:01:10.439][private$doAddFilesToCache] Destination files are [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/extracted.marker".
biodb.DEBUG[2025-02-08 17:01:10.450][self$addFilesToCache] Done adding files.
biodb.TRACE[2025-02-08 17:01:10.459][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2025-02-08 17:01:10.469][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2025-02-08 17:01:10.520][loadFileContents] Loaded 2 files from cache: [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf".
biodb.DEBUG[2025-02-08 17:01:10.531][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2025-02-08 17:01:10.568][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2025-02-08 17:01:10.581][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2025-02-08 17:01:10.622][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-08 17:01:10.626][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 17:01:10.632][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 17:01:10.718][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:10.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 17:01:10.730][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:10.740][FUN] Functions in observer BiodbConfig: [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 17:01:10.870][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 17:01:10.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 17:01:10.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:10.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:10.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 17:01:10.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 17:01:10.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:10.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:10.926][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 17:01:10.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 17:01:10.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:10.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:10.941][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 17:01:10.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 17:01:10.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:10.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:10.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 17:01:10.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 17:01:10.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:10.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:10.970][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 17:01:10.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 17:01:10.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:10.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:10.986][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 17:01:10.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 17:01:10.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:10.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.001][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 17:01:11.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 17:01:11.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.016][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 17:01:11.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 17:01:11.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.028][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 17:01:11.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 17:01:11.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.041][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 17:01:11.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 17:01:11.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.053][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 17:01:11.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 17:01:11.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 17:01:11.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 17:01:11.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.078][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 17:01:11.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 17:01:11.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 17:01:11.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 17:01:11.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 17:01:11.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 17:01:11.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 17:01:11.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 17:01:11.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-08 17:01:11.150][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-02-08 17:01:11.153][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 17:01:11.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 17:01:11.169][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:11.172][FUN] 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 17:01:11.175][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:11.177][FUN] Functions in observer BiodbConfig: [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 17:01:11.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 17:01:11.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 17:01:11.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 17:01:11.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 17:01:11.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.260][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-08 17:01:11.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-08 17:01:11.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.267][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-02-08 17:01:11.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-02-08 17:01:11.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.276][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 17:01:11.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 17:01:11.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.281][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-02-08 17:01:11.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-02-08 17:01:11.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.288][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 17:01:11.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 17:01:11.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.294][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-02-08 17:01:11.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-02-08 17:01:11.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.300][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 17:01:11.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 17:01:11.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.308][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 17:01:11.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 17:01:11.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.316][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 17:01:11.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 17:01:11.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.322][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 17:01:11.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 17:01:11.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.329][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 17:01:11.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 17:01:11.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.336][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 17:01:11.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 17:01:11.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.343][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-02-08 17:01:11.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-02-08 17:01:11.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.352][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 17:01:11.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 17:01:11.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.358][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-02-08 17:01:11.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-02-08 17:01:11.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.366][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 17:01:11.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 17:01:11.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.372][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-02-08 17:01:11.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-02-08 17:01:11.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.380][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 17:01:11.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 17:01:11.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.386][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 17:01:11.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 17:01:11.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 17:01:11.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 17:01:11.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.400][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-02-08 17:01:11.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-02-08 17:01:11.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 17:01:11.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 17:01:11.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 17:01:11.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 17:01:11.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 17:01:11.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 17:01:11.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 17:01:11.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 17:01:11.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 17:01:11.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 17:01:11.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 17:01:11.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 17:01:11.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 17:01:11.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 17:01:11.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 17:01:11.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 17:01:11.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-02-08 17:01:11.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-02-08 17:01:11.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-02-08 17:01:11.467][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2025-02-08 17:01:11.470][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-02-08 17:01:11.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-02-08 17:01:11.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.476][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-02-08 17:01:11.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-02-08 17:01:11.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.487][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-02-08 17:01:11.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-02-08 17:01:11.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.505][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-02-08 17:01:11.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-02-08 17:01:11.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.513][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-02-08 17:01:11.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-02-08 17:01:11.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.520][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-02-08 17:01:11.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-02-08 17:01:11.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-08 17:01:11.589][biodb::testThat]
biodb.INFO [2025-02-08 17:01:11.590][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-02-08 17:01:11.592][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-08 17:01:11.594][biodb::testThat]
biodb.INFO [2025-02-08 17:01:11.611][biodb::testThat]
biodb.INFO [2025-02-08 17:01:11.613][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-02-08 17:01:11.615][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-08 17:01:11.616][biodb::testThat]
biodb.WARN [2025-02-08 17:01:11.708][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-02-08 17:01:11.737][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-02-08 17:01:11.750][biodb::testThat]
biodb.INFO [2025-02-08 17:01:11.752][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-02-08 17:01:11.754][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-08 17:01:11.755][biodb::testThat]
biodb.TRACE[2025-02-08 17:01:11.804][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-08 17:01:11.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-08 17:01:11.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.813][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-08 17:01:11.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-08 17:01:11.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.819][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-02-08 17:01:11.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-02-08 17:01:11.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.826][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-02-08 17:01:11.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-02-08 17:01:11.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.874][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-08 17:01:11.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-08 17:01:11.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.880][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-02-08 17:01:11.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-02-08 17:01:11.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.886][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-02-08 17:01:11.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-02-08 17:01:11.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-02-08 17:01:11.891][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-02-08 17:01:11.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-02-08 17:01:11.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-02-08 17:01:11.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-02-08 17:01:11.912][biodb::testThat]
biodb.INFO [2025-02-08 17:01:11.914][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-02-08 17:01:11.916][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-08 17:01:11.917][biodb::testThat]
biodb.INFO [2025-02-08 17:01:11.934][biodb::testThat]
biodb.INFO [2025-02-08 17:01:11.936][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-02-08 17:01:11.938][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-08 17:01:11.939][biodb::testThat]
biodb.INFO [2025-02-08 17:01:11.953][biodb::testThat]
biodb.INFO [2025-02-08 17:01:11.956][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-02-08 17:01:11.957][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-08 17:01:11.959][biodb::testThat]
biodb.INFO [2025-02-08 17:01:11.970][biodb::testThat]
biodb.INFO [2025-02-08 17:01:11.971][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-02-08 17:01:11.973][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-02-08 17:01:11.974][biodb::testThat]
biodb.INFO [2025-02-08 17:01:11.985][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-02-08 17:01:11.988][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-02-08 17:01:11.991][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-02-08 17:01:11.993][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-02-08 17:01:11.995][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 17:01:11.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 17:01:11.998][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 17:01:12.001][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-02-08 17:01:12.043][biodb::testContext]
biodb.INFO [2025-02-08 17:01:12.045][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-08 17:01:12.047][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-02-08 17:01:12.049][biodb::testContext] ********************************************************************************
biodb.INFO [2025-02-08 17:01:12.050][biodb::testContext]
biodb.INFO [2025-02-08 17:01:12.072][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-02-08 17:01:12.076][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-02-08 17:01:12.127][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-08 17:01:12.128][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-02-08 17:01:12.130][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-02-08 17:01:12.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 17:01:12.136][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-02-08 17:01:12.138][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-02-08 17:01:12.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 17:01:12.143][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-02-08 17:01:12.145][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-02-08 17:01:12.146][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 17:01:12.150][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-02-08 17:01:12.152][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-02-08 17:01:12.153][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-02-08 17:01:12.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 17:01:12.158][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-02-08 17:01:12.160][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-02-08 17:01:12.162][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-02-08 17:01:12.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 17:01:12.168][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-02-08 17:01:12.170][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-02-08 17:01:12.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 17:01:12.176][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-02-08 17:01:12.178][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-02-08 17:01:12.179][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-02-08 17:01:12.181][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.183][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 17:01:12.185][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-02-08 17:01:12.186][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-02-08 17:01:12.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 17:01:12.191][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-02-08 17:01:12.193][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-02-08 17:01:12.195][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-02-08 17:01:12.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.199][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 17:01:12.200][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-02-08 17:01:12.202][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-02-08 17:01:12.203][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-02-08 17:01:12.205][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-02-08 17:01:12.207][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-02-08 17:01:12.209][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-02-08 17:01:12.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 17:01:12.215][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-02-08 17:01:12.216][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-02-08 17:01:12.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.220][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 17:01:12.221][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-02-08 17:01:12.223][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-02-08 17:01:12.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 17:01:12.229][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-02-08 17:01:12.231][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-02-08 17:01:12.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.237][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 17:01:12.238][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-02-08 17:01:12.240][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-02-08 17:01:12.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 17:01:12.245][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-02-08 17:01:12.247][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-02-08 17:01:12.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 17:01:12.253][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-02-08 17:01:12.255][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-02-08 17:01:12.259][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-02-08 17:01:12.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 17:01:12.264][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-02-08 17:01:12.265][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-02-08 17:01:12.267][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-02-08 17:01:12.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 17:01:12.274][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-02-08 17:01:12.278][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-08 17:01:12.280][self$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 17:01:12.282][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-08 17:01:12.284][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-08 17:01:12.285][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-08 17:01:12.287][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-08 17:01:12.289][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-08 17:01:12.291][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-08 17:01:12.292][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-08 17:01:12.294][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-08 17:01:12.301][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-08 17:01:12.303][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-02-08 17:01:12.305][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-08 17:01:12.307][self$setPropertyValue]
biodb.DEBUG[2025-02-08 17:01:12.308][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-08 17:01:12.310][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-08 17:01:12.310][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-08 17:01:12.310][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-08 17:01:12.310][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-08 17:01:12.310][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-08 17:01:12.311][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-08 17:01:12.313][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 17:01:12.314][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 17:01:12.316][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-08 17:01:12.317][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 17:01:12.318][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 17:01:12.319][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-08 17:01:12.321][self$setPropertyValue]
biodb.DEBUG[2025-02-08 17:01:12.322][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-08 17:01:12.324][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-08 17:01:12.325][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-08 17:01:12.326][self$setPropertyValue]
biodb.DEBUG[2025-02-08 17:01:12.328][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-02-08 17:01:12.330][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-08 17:01:12.332][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-02-08 17:01:12.333][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-08 17:01:12.335][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-08 17:01:12.336][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-08 17:01:12.337][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-08 17:01:12.339][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-08 17:01:12.340][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-08 17:01:12.341][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-08 17:01:12.343][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-08 17:01:12.344][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-08 17:01:12.345][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-02-08 17:01:12.347][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-08 17:01:12.348][self$setPropertyValue]
biodb.DEBUG[2025-02-08 17:01:12.349][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-08 17:01:12.351][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-02-08 17:01:12.351][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-02-08 17:01:12.351][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-02-08 17:01:12.351][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-02-08 17:01:12.351][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-02-08 17:01:12.352][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-08 17:01:12.353][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 17:01:12.354][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 17:01:12.356][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-08 17:01:12.357][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 17:01:12.359][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 17:01:12.360][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-08 17:01:12.362][self$setPropertyValue]
biodb.DEBUG[2025-02-08 17:01:12.364][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-08 17:01:12.365][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-08 17:01:12.366][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-08 17:01:12.367][self$setPropertyValue]
biodb.DEBUG[2025-02-08 17:01:12.370][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-02-08 17:01:12.372][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-08 17:01:12.374][self$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 17:01:12.375][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-08 17:01:12.377][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-08 17:01:12.378][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-08 17:01:12.379][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-08 17:01:12.381][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-08 17:01:12.382][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-08 17:01:12.383][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-02-08 17:01:12.385][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-08 17:01:12.386][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-08 17:01:12.388][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-02-08 17:01:12.389][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-08 17:01:12.391][self$setPropertyValue]
biodb.DEBUG[2025-02-08 17:01:12.392][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-08 17:01:12.394][self$setPropertyValue]
biodb.DEBUG[2025-02-08 17:01:12.395][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-08 17:01:12.396][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 17:01:12.397][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 17:01:12.399][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-08 17:01:12.400][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 17:01:12.401][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 17:01:12.403][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-08 17:01:12.404][self$setPropertyValue]
biodb.DEBUG[2025-02-08 17:01:12.405][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-08 17:01:12.406][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-08 17:01:12.408][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-08 17:01:12.409][self$setPropertyValue]
biodb.DEBUG[2025-02-08 17:01:12.410][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-02-08 17:01:12.412][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-02-08 17:01:12.415][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-02-08 17:01:12.417][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-08 17:01:12.418][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-08 17:01:12.419][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-02-08 17:01:12.421][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-02-08 17:01:12.422][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-02-08 17:01:12.423][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-08 17:01:12.425][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-02-08 17:01:12.426][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-08 17:01:12.428][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-02-08 17:01:12.430][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-02-08 17:01:12.431][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-08 17:01:12.432][self$setPropertyValue]
biodb.DEBUG[2025-02-08 17:01:12.434][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-02-08 17:01:12.435][self$setPropertyValue]
biodb.DEBUG[2025-02-08 17:01:12.436][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-02-08 17:01:12.438][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 17:01:12.439][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 17:01:12.440][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-08 17:01:12.441][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 17:01:12.443][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 17:01:12.444][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-08 17:01:12.445][self$setPropertyValue]
biodb.DEBUG[2025-02-08 17:01:12.447][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-08 17:01:12.448][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-08 17:01:12.449][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-02-08 17:01:12.450][self$setPropertyValue]
biodb.DEBUG[2025-02-08 17:01:12.453][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-08 17:01:12.455][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 17:01:12.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.460][FUN] 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 17:01:12.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 17:01:12.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.466][FUN] 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 17:01:12.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 17:01:12.470][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.473][FUN] 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 17:01:12.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.476][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.DEBUG[2025-02-08 17:01:12.477][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.479][FUN] 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 17:01:12.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 17:01:12.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 17:01:12.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 17:01:12.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.492][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 17:01:12.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 17:01:12.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.498][FUN] 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 17:01:12.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 17:01:12.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 17:01:12.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 17:01:12.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 17:01:12.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 17:01:12.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 17:01:12.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 17:01:12.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.522][FUN] 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 17:01:12.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 17:01:12.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.530][FUN] 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 17:01:12.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 17:01:12.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.536][FUN] 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 17:01:12.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 17:01:12.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 17:01:12.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 17:01:12.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-02-08 17:01:12.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 17:01:12.552][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.555][FUN] 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 17:01:12.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 17:01:12.559][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.561][FUN] 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 17:01:12.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 17:01:12.565][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-02-08 17:01:12.570][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-02-08 17:01:12.571][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-02-08 17:01:12.573][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-02-08 17:01:12.575][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-02-08 17:01:12.577][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-02-08 17:01:12.578][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-02-08 17:01:12.580][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-02-08 17:01:12.582][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-02-08 17:01:12.585][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-02-08 17:01:12.587][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-02-08 17:01:12.589][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-02-08 17:01:12.591][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-02-08 17:01:12.593][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-02-08 17:01:12.595][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-02-08 17:01:12.596][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-02-08 17:01:12.599][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-02-08 17:01:12.601][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-02-08 17:01:12.602][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-02-08 17:01:12.605][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-02-08 17:01:12.607][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-02-08 17:01:12.609][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-02-08 17:01:12.610][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-02-08 17:01:12.613][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-02-08 17:01:12.615][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-02-08 17:01:12.617][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-02-08 17:01:12.619][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-02-08 17:01:12.620][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-02-08 17:01:12.622][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-02-08 17:01:12.624][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-02-08 17:01:12.626][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-02-08 17:01:12.628][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-02-08 17:01:12.630][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-02-08 17:01:12.631][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-02-08 17:01:12.633][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-02-08 17:01:12.635][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-02-08 17:01:12.638][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-02-08 17:01:12.640][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-02-08 17:01:12.641][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-02-08 17:01:12.643][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-02-08 17:01:12.645][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-02-08 17:01:12.647][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-02-08 17:01:12.649][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-02-08 17:01:12.651][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-02-08 17:01:12.653][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-02-08 17:01:12.654][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-02-08 17:01:12.656][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-02-08 17:01:12.658][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-02-08 17:01:12.660][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-02-08 17:01:12.662][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-02-08 17:01:12.664][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-02-08 17:01:12.666][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-02-08 17:01:12.668][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-02-08 17:01:12.670][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-02-08 17:01:12.671][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-02-08 17:01:12.673][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-02-08 17:01:12.675][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-02-08 17:01:12.677][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-02-08 17:01:12.680][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-02-08 17:01:12.682][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-02-08 17:01:12.683][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-02-08 17:01:12.685][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-02-08 17:01:12.687][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-02-08 17:01:12.689][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-02-08 17:01:12.692][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-02-08 17:01:12.694][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-02-08 17:01:12.695][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-02-08 17:01:12.697][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-02-08 17:01:12.699][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-02-08 17:01:12.701][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-02-08 17:01:12.702][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-02-08 17:01:12.705][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-02-08 17:01:12.706][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-02-08 17:01:12.708][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-02-08 17:01:12.710][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-02-08 17:01:12.711][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-02-08 17:01:12.713][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-02-08 17:01:12.715][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-02-08 17:01:12.718][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-02-08 17:01:12.720][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-02-08 17:01:12.721][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-02-08 17:01:12.723][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-02-08 17:01:12.725][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-02-08 17:01:12.727][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-02-08 17:01:12.730][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-02-08 17:01:12.732][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-02-08 17:01:12.734][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.735][FUN] 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 17:01:12.736][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 17:01:12.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 17:01:12.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 17:01:12.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.744][FUN] 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 17:01:12.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 17:01:12.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 17:01:12.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 17:01:12.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.755][FUN] 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 17:01:12.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 17:01:12.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 17:01:12.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 17:01:12.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.764][FUN] 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 17:01:12.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 17:01:12.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 17:01:12.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 17:01:12.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.772][FUN] 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 17:01:12.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 17:01:12.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 17:01:12.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 17:01:12.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.781][FUN] 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 17:01:12.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.783][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 17:01:12.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 17:01:12.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 17:01:12.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.789][FUN] 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 17:01:12.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 17:01:12.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 17:01:12.795][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 17:01:12.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.797][FUN] 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 17:01:12.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 17:01:12.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 17:01:12.804][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 17:01:12.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.806][FUN] 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 17:01:12.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 17:01:12.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 17:01:12.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 17:01:12.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.815][FUN] 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 17:01:12.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 17:01:12.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 17:01:12.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 17:01:12.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.824][FUN] 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 17:01:12.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 17:01:12.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 17:01:12.832][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 17:01:12.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.835][FUN] 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 17:01:12.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 17:01:12.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 17:01:12.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 17:01:12.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.843][FUN] 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 17:01:12.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 17:01:12.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 17:01:12.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 17:01:12.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.851][FUN] 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 17:01:12.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 17:01:12.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 17:01:12.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 17:01:12.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.860][FUN] 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 17:01:12.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 17:01:12.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 17:01:12.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 17:01:12.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.869][FUN] 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 17:01:12.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 17:01:12.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 17:01:12.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 17:01:12.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.877][FUN] 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 17:01:12.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 17:01:12.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-02-08 17:01:12.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 17:01:12.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 17:01:12.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:12.885][FUN] 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 17:01:12.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:12.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-02-08 17:01:12.914][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-02-08 17:01:12.927][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-02-08 17:01:12.930][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-02-08 17:01:12.932][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-02-08 17:01:12.933][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-02-08 17:01:12.935][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-02-08 17:01:12.936][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-02-08 17:01:12.937][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-02-08 17:01:12.938][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-02-08 17:01:12.940][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-02-08 17:01:12.941][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-02-08 17:01:12.942][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-02-08 17:01:12.944][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-02-08 17:01:12.945][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-02-08 17:01:12.947][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-02-08 17:01:12.950][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-02-08 17:01:12.950][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-02-08 17:01:12.950][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-02-08 17:01:12.950][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-02-08 17:01:12.950][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-02-08 17:01:12.950][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-02-08 17:01:12.950][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-02-08 17:01:12.951][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-02-08 17:01:12.953][self$setPropertyValue]
biodb.DEBUG[2025-02-08 17:01:12.954][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-02-08 17:01:12.955][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 17:01:12.957][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 17:01:12.958][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-02-08 17:01:12.960][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-02-08 17:01:12.961][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-02-08 17:01:12.962][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-02-08 17:01:12.964][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-02-08 17:01:12.964][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-02-08 17:01:12.964][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-02-08 17:01:12.964][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-02-08 17:01:12.965][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-02-08 17:01:12.966][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-02-08 17:01:12.968][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-02-08 17:01:12.969][self$setPropertyValue]
biodb.DEBUG[2025-02-08 17:01:12.971][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-02-08 17:01:12.978][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-02-08 17:01:12.980][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-02-08 17:01:12.982][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-02-08 17:01:12.985][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-02-08 17:01:12.987][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-08 17:01:12.989][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-02-08 17:01:12.990][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-02-08 17:01:12.992][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-02-08 17:01:12.994][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-02-08 17:01:12.995][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-02-08 17:01:12.997][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-02-08 17:01:12.998][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-02-08 17:01:12.999][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-02-08 17:01:13.000][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-02-08 17:01:13.002][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-02-08 17:01:13.003][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-02-08 17:01:13.004][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-02-08 17:01:13.006][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 17:01:13.007][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-02-08 17:01:13.008][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".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ]
> 
> proc.time()
   user  system elapsed 
1252.68  447.53 3320.10

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --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 'E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck'
* using R Under development (unstable) (2025-01-21 r87610 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 whether package 'biodbNci' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 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 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
  'E:/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__~1.EXE (GCC) 13.3.0'
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -DR_NO_REMAP -c extractEntries.cpp -o extractEntries.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -DR_NO_REMAP -c test-100-example.cpp -o test-100-example.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/testthat/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -DR_NO_REMAP -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -shared -s -static-libgcc -o biodbNci.dll tmp.def RcppExports.o extractEntries.o test-100-example.o test-runner.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbNci)