Back to Long Tests report for BioC 3.21

This page was generated on 2025-01-11 23:55 -0500 (Sat, 11 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4760
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4479
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4443
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: 2025-01-11 09:55 -0500 (Sat, 11 Jan 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: 2025-01-11 16:04:22 -0500 (Sat, 11 Jan 2025)
EndedAt: 2025-01-11 17:25:11 -0500 (Sat, 11 Jan 2025)
EllapsedTime: 4849.7 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbNci.Rcheck
Warnings: 0

Tests output

biodbNci.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 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 [2025-01-11 16:05:39.248][biodb::testContext]
biodb.INFO [2025-01-11 16:05:39.251][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-11 16:05:39.252][biodb::testContext] Test context - Generic long tests
biodb.INFO [2025-01-11 16:05:39.254][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-11 16:05:39.255][biodb::testContext]
biodb.INFO [2025-01-11 16:05:39.261][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-01-11 16:05:39.264][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-01-11 16:05:39.271][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-11 16:05:39.273][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-11 16:05:39.274][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-11 16:05:39.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.278][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-11 16:05:39.294][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-11 16:05:39.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.299][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-11 16:05:39.300][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-11 16:05:39.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.304][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-11 16:05:39.305][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-11 16:05:39.307][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-11 16:05:39.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.311][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-11 16:05:39.312][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-11 16:05:39.313][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-11 16:05:39.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.318][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-11 16:05:39.319][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-11 16:05:39.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.323][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-11 16:05:39.324][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-11 16:05:39.326][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-11 16:05:39.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.330][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-11 16:05:39.331][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-11 16:05:39.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.335][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-11 16:05:39.337][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-11 16:05:39.338][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-11 16:05:39.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.342][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-11 16:05:39.343][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-11 16:05:39.345][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-11 16:05:39.346][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-11 16:05:39.347][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-11 16:05:39.348][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-11 16:05:39.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.353][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-11 16:05:39.354][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-11 16:05:39.356][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.359][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-11 16:05:39.360][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-11 16:05:39.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.364][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-11 16:05:39.366][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-11 16:05:39.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.370][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-11 16:05:39.371][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-11 16:05:39.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.376][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-11 16:05:39.377][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-11 16:05:39.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.381][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-11 16:05:39.382][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-11 16:05:39.386][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-11 16:05:39.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.390][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-11 16:05:39.391][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-11 16:05:39.393][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-11 16:05:39.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.399][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-11 16:05:39.426][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-11 16:05:39.447][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-01-11 16:05:39.448][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-11 16:05:39.450][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-11 16:05:39.451][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-11 16:05:39.452][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-11 16:05:39.453][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-11 16:05:39.454][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-11 16:05:39.456][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-11 16:05:39.457][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-11 16:05:39.458][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-11 16:05:39.459][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-11 16:05:39.460][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-11 16:05:39.461][self$setPropertyValue]
biodb.DEBUG[2025-01-11 16:05:39.463][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-11 16:05:39.464][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-11 16:05:39.464][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-11 16:05:39.464][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-11 16:05:39.464][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-11 16:05:39.464][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-11 16:05:39.465][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-11 16:05:39.466][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-11 16:05:39.468][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-11 16:05:39.469][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-11 16:05:39.470][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-11 16:05:39.471][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-11 16:05:39.472][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-11 16:05:39.473][self$setPropertyValue]
biodb.DEBUG[2025-01-11 16:05:39.474][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-11 16:05:39.475][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-11 16:05:39.477][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-11 16:05:39.478][self$setPropertyValue]
biodb.DEBUG[2025-01-11 16:05:39.479][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-11 16:05:39.481][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-11 16:05:39.482][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-11 16:05:39.483][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-11 16:05:39.485][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-11 16:05:39.486][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-11 16:05:39.487][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-11 16:05:39.488][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-11 16:05:39.489][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-11 16:05:39.491][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-11 16:05:39.492][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-11 16:05:39.493][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-11 16:05:39.494][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-11 16:05:39.495][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-11 16:05:39.497][self$setPropertyValue]
biodb.DEBUG[2025-01-11 16:05:39.498][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-11 16:05:39.499][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-11 16:05:39.499][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-11 16:05:39.499][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-11 16:05:39.499][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-11 16:05:39.499][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-11 16:05:39.500][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-11 16:05:39.501][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-11 16:05:39.502][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-11 16:05:39.504][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-11 16:05:39.505][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-11 16:05:39.506][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-11 16:05:39.507][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-11 16:05:39.508][self$setPropertyValue]
biodb.DEBUG[2025-01-11 16:05:39.509][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-11 16:05:39.510][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-11 16:05:39.511][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-11 16:05:39.513][self$setPropertyValue]
biodb.DEBUG[2025-01-11 16:05:39.514][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-11 16:05:39.516][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-11 16:05:39.517][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-01-11 16:05:39.518][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-11 16:05:39.519][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-11 16:05:39.521][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-11 16:05:39.522][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-11 16:05:39.523][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-11 16:05:39.524][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-11 16:05:39.525][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-11 16:05:39.527][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-11 16:05:39.528][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-11 16:05:39.529][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-11 16:05:39.530][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-11 16:05:39.531][self$setPropertyValue]
biodb.DEBUG[2025-01-11 16:05:39.532][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-11 16:05:39.534][self$setPropertyValue]
biodb.DEBUG[2025-01-11 16:05:39.535][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-11 16:05:39.536][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-11 16:05:39.537][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-11 16:05:39.538][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-11 16:05:39.539][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-11 16:05:39.540][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-11 16:05:39.542][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-11 16:05:39.543][self$setPropertyValue]
biodb.DEBUG[2025-01-11 16:05:39.544][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-11 16:05:39.545][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-11 16:05:39.546][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-11 16:05:39.547][self$setPropertyValue]
biodb.DEBUG[2025-01-11 16:05:39.549][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-11 16:05:39.550][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-11 16:05:39.552][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-11 16:05:39.553][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-11 16:05:39.554][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-11 16:05:39.555][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-11 16:05:39.556][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-11 16:05:39.558][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-11 16:05:39.559][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-11 16:05:39.560][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-11 16:05:39.561][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-11 16:05:39.562][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-11 16:05:39.563][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-11 16:05:39.565][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-11 16:05:39.566][self$setPropertyValue]
biodb.DEBUG[2025-01-11 16:05:39.567][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-11 16:05:39.568][self$setPropertyValue]
biodb.DEBUG[2025-01-11 16:05:39.569][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-11 16:05:39.570][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-11 16:05:39.572][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-11 16:05:39.573][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-11 16:05:39.574][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-11 16:05:39.575][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-11 16:05:39.576][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-11 16:05:39.577][self$setPropertyValue]
biodb.DEBUG[2025-01-11 16:05:39.578][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-11 16:05:39.579][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-11 16:05:39.581][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-11 16:05:39.582][self$setPropertyValue]
biodb.DEBUG[2025-01-11 16:05:39.585][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-11 16:05:39.586][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.679][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.690][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-11 16:05:39.694][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-11 16:05:39.695][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-11 16:05:39.697][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-11 16:05:39.699][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-11 16:05:39.700][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-11 16:05:39.702][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-11 16:05:39.703][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-11 16:05:39.705][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-11 16:05:39.706][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-11 16:05:39.708][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-11 16:05:39.709][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-11 16:05:39.711][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-11 16:05:39.712][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-11 16:05:39.714][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-11 16:05:39.716][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-11 16:05:39.717][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-11 16:05:39.719][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-11 16:05:39.720][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-11 16:05:39.722][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-11 16:05:39.723][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-11 16:05:39.725][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-11 16:05:39.726][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-11 16:05:39.728][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-11 16:05:39.730][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-11 16:05:39.731][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-11 16:05:39.733][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-11 16:05:39.734][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-11 16:05:39.736][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-11 16:05:39.737][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-11 16:05:39.739][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-11 16:05:39.740][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-11 16:05:39.742][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-11 16:05:39.743][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-11 16:05:39.745][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-11 16:05:39.747][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-11 16:05:39.748][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-11 16:05:39.750][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-11 16:05:39.751][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-11 16:05:39.753][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-11 16:05:39.754][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-11 16:05:39.756][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-11 16:05:39.757][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-11 16:05:39.759][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-11 16:05:39.761][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-11 16:05:39.762][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-11 16:05:39.764][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-11 16:05:39.765][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-11 16:05:39.767][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-11 16:05:39.768][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-11 16:05:39.770][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-11 16:05:39.771][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-11 16:05:39.773][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-11 16:05:39.774][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-11 16:05:39.776][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-11 16:05:39.778][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-11 16:05:39.779][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-11 16:05:39.781][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-11 16:05:39.782][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-11 16:05:39.784][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-11 16:05:39.785][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-11 16:05:39.787][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-11 16:05:39.788][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-11 16:05:39.790][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-11 16:05:39.792][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-11 16:05:39.793][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-11 16:05:39.795][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-11 16:05:39.796][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-11 16:05:39.798][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-11 16:05:39.799][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-11 16:05:39.801][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-11 16:05:39.802][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-11 16:05:39.804][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-11 16:05:39.805][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-11 16:05:39.807][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-11 16:05:39.809][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-11 16:05:39.810][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-11 16:05:39.812][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-11 16:05:39.813][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-11 16:05:39.815][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-11 16:05:39.816][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-11 16:05:39.818][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-11 16:05:39.819][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-11 16:05:39.842][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-11 16:05:39.845][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-01-11 16:05:39.848][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-11 16:05:39.849][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.851][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 16:05:39.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 16:05:39.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 16:05:39.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 16:05:39.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.871][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[2025-01-11 16:05:39.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 16:05:39.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 16:05:39.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 16:05:39.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 16:05:39.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 16:05:39.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 16:05:39.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 16:05:39.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 16:05:39.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 16:05:39.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 16:05:39.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 16:05:39.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 16:05:39.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 16:05:39.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 16:05:39.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 16:05:39.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 16:05:39.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 16:05:39.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 16:05:39.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 16:05:39.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 16:05:39.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 16:05:39.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 16:05:39.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 16:05:39.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 16:05:39.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.967][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 16:05:39.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 16:05:39.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 16:05:39.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 16:05:39.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 16:05:39.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 16:05:39.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 16:05:39.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:39.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:39.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:39.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 16:05:39.991][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-01-11 16:05:40.000][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-01-11 16:05:40.002][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-11 16:05:40.003][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-01-11 16:05:40.005][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-11 16:05:40.006][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-11 16:05:40.007][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-01-11 16:05:40.008][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-01-11 16:05:40.009][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-11 16:05:40.010][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-11 16:05:40.012][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-01-11 16:05:40.013][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-11 16:05:40.014][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-11 16:05:40.015][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-01-11 16:05:40.016][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-11 16:05:40.018][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-01-11 16:05:40.018][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-01-11 16:05:40.018][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-01-11 16:05:40.018][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-01-11 16:05:40.018][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-01-11 16:05:40.018][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-01-11 16:05:40.018][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-01-11 16:05:40.019][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-11 16:05:40.020][self$setPropertyValue]
biodb.DEBUG[2025-01-11 16:05:40.021][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-11 16:05:40.022][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-11 16:05:40.023][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-11 16:05:40.025][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-11 16:05:40.026][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-11 16:05:40.027][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-11 16:05:40.028][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-11 16:05:40.029][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-01-11 16:05:40.029][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-01-11 16:05:40.029][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-01-11 16:05:40.029][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-01-11 16:05:40.030][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-11 16:05:40.031][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-11 16:05:40.032][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-11 16:05:40.034][self$setPropertyValue]
biodb.DEBUG[2025-01-11 16:05:40.039][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-01-11 16:05:40.060][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-01-11 16:05:40.062][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-01-11 16:05:40.065][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-01-11 16:05:40.069][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-01-11 16:05:40.073][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-11 16:05:40.074][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-11 16:05:40.075][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-01-11 16:05:40.077][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-01-11 16:05:40.079][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-01-11 16:05:40.080][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-01-11 16:05:40.122][biodb::testThat]
biodb.INFO [2025-01-11 16:05:40.123][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-01-11 16:05:40.124][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-11 16:05:40.125][biodb::testThat]
biodb.TRACE[2025-01-11 16:05:40.130][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[2025-01-11 16:05:40.132][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-01-11 16:05:40.135][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-01-11 16:05:40.142][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-11 16:05:40.143][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 16:05:40.144][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 16:05:40.160][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:40.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:40.163][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:40.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-11 16:05:40.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:40.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:40.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.199][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-11 16:05:40.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-11 16:05:40.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.225][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-11 16:05:40.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-11 16:05:40.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.230][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-11 16:05:40.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-11 16:05:40.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.235][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-11 16:05:40.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-11 16:05:40.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.241][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-11 16:05:40.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-11 16:05:40.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.245][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-11 16:05:40.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-11 16:05:40.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.251][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-11 16:05:40.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-11 16:05:40.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.255][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-11 16:05:40.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-11 16:05:40.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.261][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-11 16:05:40.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-11 16:05:40.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.265][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-11 16:05:40.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-11 16:05:40.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:40.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.275][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-11 16:05:40.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-11 16:05:40.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:40.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:40.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:40.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:40.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:40.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:40.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-11 16:05:40.343][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2025-01-11 16:05:40.346][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-11 16:05:40.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-11 16:05:40.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.351][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-11 16:05:40.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-11 16:05:40.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.358][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-11 16:05:40.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-11 16:05:40.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.363][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-11 16:05:40.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-11 16:05:40.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:40.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.405][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-11 16:05:40.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-11 16:05:40.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:40.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:40.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:40.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:40.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:40.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:40.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.446][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-11 16:05:40.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-11 16:05:40.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.451][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-11 16:05:40.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-11 16:05:40.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.456][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-11 16:05:40.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-11 16:05:40.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:40.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:40.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:40.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.489][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.490][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:40.491][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.493][ef$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:40.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.509][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-11 16:05:40.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-11 16:05:40.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.513][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-11 16:05:40.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-11 16:05:40.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.518][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-11 16:05:40.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-11 16:05:40.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.523][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-11 16:05:40.524][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-11 16:05:40.525][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.526][ef$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.527][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-11 16:05:40.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-11 16:05:40.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.542][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-11 16:05:40.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-11 16:05:40.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.547][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-11 16:05:40.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-11 16:05:40.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.552][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-11 16:05:40.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-11 16:05:40.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.556][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-11 16:05:40.558][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-11 16:05:40.559][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.560][ef$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.561][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-11 16:05:40.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-11 16:05:40.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.575][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-11 16:05:40.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-11 16:05:40.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.580][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-11 16:05:40.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-11 16:05:40.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.585][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-11 16:05:40.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-11 16:05:40.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.590][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-11 16:05:40.591][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-11 16:05:40.592][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.593][ef$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.595][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-11 16:05:40.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-11 16:05:40.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.609][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-11 16:05:40.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-11 16:05:40.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.614][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-11 16:05:40.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-11 16:05:40.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.619][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-11 16:05:40.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-11 16:05:40.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.624][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-11 16:05:40.625][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-11 16:05:40.626][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.627][ef$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.628][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-11 16:05:40.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-11 16:05:40.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.643][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.644][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:40.645][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.646][ef$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.658][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-11 16:05:40.659][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-11 16:05:40.661][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.662][ef$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.668][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-11 16:05:40.670][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-11 16:05:40.671][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.672][ef$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.679][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-11 16:05:40.680][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-11 16:05:40.681][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.682][ef$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.689][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-11 16:05:40.690][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-11 16:05:40.691][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.692][ef$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.711][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[2025-01-11 16:05:40.740][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2025-01-11 16:05:40.742][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2025-01-11 16:05:40.744][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-11 16:05:40.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 16:05:40.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 16:05:40.753][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 16:05:40.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 16:05:40.755][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-11 16:05:40.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-11 16:05:40.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:40.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:40.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.790][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-11 16:05:40.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-11 16:05:40.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.800][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-11 16:05:40.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-11 16:05:40.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.805][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-11 16:05:40.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-11 16:05:40.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.810][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-11 16:05:40.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-11 16:05:40.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.816][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-11 16:05:40.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-11 16:05:40.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.821][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-11 16:05:40.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-11 16:05:40.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.826][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-11 16:05:40.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-11 16:05:40.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.831][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-11 16:05:40.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-11 16:05:40.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.836][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-11 16:05:40.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-11 16:05:40.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.841][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-11 16:05:40.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-11 16:05:40.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.845][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-11 16:05:40.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-11 16:05:40.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.850][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-11 16:05:40.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-11 16:05:40.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.855][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-11 16:05:40.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-11 16:05:40.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.861][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-11 16:05:40.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-11 16:05:40.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.865][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-11 16:05:40.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-11 16:05:40.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.871][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-11 16:05:40.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-11 16:05:40.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.875][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-11 16:05:40.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-11 16:05:40.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.881][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-11 16:05:40.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-11 16:05:40.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.886][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-11 16:05:40.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-11 16:05:40.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:40.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.895][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-11 16:05:40.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-11 16:05:40.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:40.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:40.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:40.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:40.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:40.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:40.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-11 16:05:40.929][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2025-01-11 16:05:40.947][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-11 16:05:40.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-11 16:05:40.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.952][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-11 16:05:40.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-11 16:05:40.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.956][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-11 16:05:40.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-11 16:05:40.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.966][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-11 16:05:40.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-11 16:05:40.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:40.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.982][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-11 16:05:40.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-11 16:05:40.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:40.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:40.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:40.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:40.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:41.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:41.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:41.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:41.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:41.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:41.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:41.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:41.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:41.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.023][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-11 16:05:41.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-11 16:05:41.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.028][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-11 16:05:41.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-11 16:05:41.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.032][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-11 16:05:41.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-11 16:05:41.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:41.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:41.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:41.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:41.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:41.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:41.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.069][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:41.070][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:41.071][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.072][ef$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:41.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:41.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.088][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-11 16:05:41.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-11 16:05:41.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.093][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-11 16:05:41.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-11 16:05:41.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.097][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-11 16:05:41.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-11 16:05:41.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.102][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-11 16:05:41.103][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-11 16:05:41.105][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.106][ef$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.107][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-11 16:05:41.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-11 16:05:41.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.121][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-11 16:05:41.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-11 16:05:41.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.126][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-11 16:05:41.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-11 16:05:41.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.131][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-11 16:05:41.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-11 16:05:41.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.136][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-11 16:05:41.142][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-11 16:05:41.143][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.145][ef$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.146][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-11 16:05:41.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-11 16:05:41.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.160][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-11 16:05:41.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-11 16:05:41.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.165][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-11 16:05:41.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-11 16:05:41.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.170][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-11 16:05:41.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-11 16:05:41.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.175][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-11 16:05:41.176][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-11 16:05:41.177][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.178][ef$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.179][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-11 16:05:41.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-11 16:05:41.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.194][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-11 16:05:41.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-11 16:05:41.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.199][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-11 16:05:41.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-11 16:05:41.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.203][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-11 16:05:41.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-11 16:05:41.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.208][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-11 16:05:41.209][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-11 16:05:41.210][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.212][ef$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.213][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-11 16:05:41.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-11 16:05:41.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.227][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-11 16:05:41.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-11 16:05:41.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.233][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-11 16:05:41.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-11 16:05:41.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.237][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-11 16:05:41.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-11 16:05:41.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.242][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-11 16:05:41.243][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-11 16:05:41.244][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.246][ef$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.247][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-11 16:05:41.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-11 16:05:41.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.261][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-11 16:05:41.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-11 16:05:41.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.266][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-11 16:05:41.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-11 16:05:41.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.271][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-11 16:05:41.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-11 16:05:41.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.276][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-11 16:05:41.277][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-11 16:05:41.278][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.279][ef$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.281][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-11 16:05:41.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-11 16:05:41.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.295][ef$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 16:05:41.297][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 16:05:41.298][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.299][ef$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.306][ef$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-11 16:05:41.307][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-11 16:05:41.308][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.309][ef$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.316][ef$get] Asked field names are: formula.
biodb.TRACE[2025-01-11 16:05:41.317][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-11 16:05:41.318][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.319][ef$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.331][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-01-11 16:05:41.332][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-11 16:05:41.334][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.335][ef$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.342][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-11 16:05:41.343][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-11 16:05:41.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.345][ef$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.352][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-11 16:05:41.354][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-11 16:05:41.356][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.358][ef$get] fields variable is a list.
biodb.TRACE[2025-01-11 16:05:41.365][ef$get] Asked field names are: name.
biodb.TRACE[2025-01-11 16:05:41.366][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-01-11 16:05:41.368][ef$get] 1 fields were returned.
biodb.TRACE[2025-01-11 16:05:41.369][ef$get] fields variable is a list.
biodb.INFO [2025-01-11 16:05:41.382][biodb::testThat]
biodb.INFO [2025-01-11 16:05:41.383][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-01-11 16:05:41.384][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-11 16:05:41.385][biodb::testThat]
biodb.DEBUG[2025-01-11 16:05:41.388][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2025-01-11 16:05:41.394][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.INFO [2025-01-11 16:05:41.400][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427" for "nci.cactus-8efc65070d01b214e760b1d4932ee427".
biodb.DEBUG[2025-01-11 16:05:41.402][self$isDownloaded] Database nci.cactus has not yet been downloaded.
biodb.INFO [2025-01-11 16:05:41.403][self$download] Downloading whole database of nci.cactus.
biodb.INFO [2025-01-11 16:05:41.405][private$doDownload] Downloading NCI CACTUS database at "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz" ...
biodb.DEBUG[2025-01-11 16:05:41.407][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[2025-01-11 16:05:51.242][cch$addFilesToCache] Moving files to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp\nci.cactus15b9c7b42411agz".
biodb.TRACE[2025-01-11 16:05:51.244][private$doAddFilesToCache] Destination files are [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2025-01-11 16:05:51.263][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2025-01-11 16:05:51.266][self$getDownloadPath] Download path of nci.cactus is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2025-01-11 16:05:51.267][self$download] Downloading of nci.cactus completed.
biodb.TRACE[2025-01-11 16:05:51.271][self$addFilesToCache] Moving files to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp\marker15b9c77061958marker".
biodb.TRACE[2025-01-11 16:05:51.272][private$doAddFilesToCache] Destination files are [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/downloaded.marker".
biodb.DEBUG[2025-01-11 16:05:51.280][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-01-11 16:05:51.282][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2025-01-11 16:05:51.283][self$download] Extract whole database of nci.cactus.
biodb.INFO [2025-01-11 16:05:51.284][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.DEBUG[2025-01-11 16:05:51.286][self$getDownloadPath] Download path of nci.cactus is "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2025-01-11 16:07:55.482][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2025-01-11 16:07:55.485][private$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[2025-01-11 17:06:28.383][self$addFilesToCache] Moving files to cache [265242]: "C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/entry_1.txt, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/entry_2.txt, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/entry_3.txt, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/entry_4.txt, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/entry_5.txt, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/entry_6.txt, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/entry_7.txt, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/entry_8.txt, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/entry_9.txt, C:\Users\biocbuild\AppData\Local\R\cache\R\biodb\tmp/entry_10.txt, ...".
biodb.TRACE[2025-01-11 17:06:28.900][private$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[2025-01-11 17:25:07.235][self$addFilesToCache] Done adding files.
biodb.DEBUG[2025-01-11 17:25:07.313][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2025-01-11 17:25:07.482][self$addFilesToCache] Moving files to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/tmp\marker15b9c16d31efamarker".
biodb.TRACE[2025-01-11 17:25:07.487][private$doAddFilesToCache] Destination files are [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/extracted.marker".
biodb.DEBUG[2025-01-11 17:25:07.501][self$addFilesToCache] Done adding files.
biodb.TRACE[2025-01-11 17:25:07.509][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2025-01-11 17:25:07.515][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2025-01-11 17:25:07.562][loadFileContents] Loaded 2 files from cache: [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf".
biodb.DEBUG[2025-01-11 17:25:07.572][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2025-01-11 17:25:07.609][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2025-01-11 17:25:07.621][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2025-01-11 17:25:07.661][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-11 17:25:07.664][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 17:25:07.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 17:25:07.765][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:07.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:07.774][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:07.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-11 17:25:07.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 17:25:07.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 17:25:07.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:07.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:07.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 17:25:07.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 17:25:07.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:07.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:07.885][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-11 17:25:07.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-11 17:25:07.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:07.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:07.901][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-11 17:25:07.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-11 17:25:07.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:07.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:07.915][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-11 17:25:07.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-11 17:25:07.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:07.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:07.927][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-11 17:25:07.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-11 17:25:07.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:07.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:07.941][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-11 17:25:07.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-11 17:25:07.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:07.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:07.955][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-11 17:25:07.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-11 17:25:07.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:07.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:07.970][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-11 17:25:07.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-11 17:25:07.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:07.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:07.982][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-11 17:25:07.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-11 17:25:07.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:07.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:07.997][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-11 17:25:08.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-11 17:25:08.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.008][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-11 17:25:08.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-11 17:25:08.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 17:25:08.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 17:25:08.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.030][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-11 17:25:08.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-11 17:25:08.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 17:25:08.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 17:25:08.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 17:25:08.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 17:25:08.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 17:25:08.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 17:25:08.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-11 17:25:08.089][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-01-11 17:25:08.092][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 17:25:08.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 17:25:08.109][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:08.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:08.114][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:08.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-01-11 17:25:08.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 17:25:08.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 17:25:08.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 17:25:08.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 17:25:08.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.174][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-11 17:25:08.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-11 17:25:08.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.180][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2025-01-11 17:25:08.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2025-01-11 17:25:08.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.191][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-11 17:25:08.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-11 17:25:08.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.197][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-01-11 17:25:08.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-01-11 17:25:08.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.203][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-11 17:25:08.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-11 17:25:08.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.209][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-01-11 17:25:08.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-01-11 17:25:08.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.215][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-11 17:25:08.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-11 17:25:08.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.221][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-11 17:25:08.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-11 17:25:08.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.227][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-11 17:25:08.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-11 17:25:08.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.233][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-11 17:25:08.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-11 17:25:08.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.238][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-11 17:25:08.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-11 17:25:08.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.244][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-11 17:25:08.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-11 17:25:08.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.251][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-01-11 17:25:08.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-01-11 17:25:08.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.257][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-11 17:25:08.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-11 17:25:08.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.263][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-01-11 17:25:08.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-01-11 17:25:08.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.270][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-11 17:25:08.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-11 17:25:08.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.275][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-01-11 17:25:08.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-01-11 17:25:08.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.283][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-11 17:25:08.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-11 17:25:08.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.290][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-11 17:25:08.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-11 17:25:08.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 17:25:08.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 17:25:08.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.302][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2025-01-11 17:25:08.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2025-01-11 17:25:08.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 17:25:08.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 17:25:08.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 17:25:08.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 17:25:08.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 17:25:08.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 17:25:08.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 17:25:08.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 17:25:08.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 17:25:08.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 17:25:08.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 17:25:08.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 17:25:08.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 17:25:08.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 17:25:08.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 17:25:08.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 17:25:08.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-01-11 17:25:08.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-01-11 17:25:08.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-01-11 17:25:08.366][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2025-01-11 17:25:08.368][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-01-11 17:25:08.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-01-11 17:25:08.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.375][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-01-11 17:25:08.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-01-11 17:25:08.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.384][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-01-11 17:25:08.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-01-11 17:25:08.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.402][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-01-11 17:25:08.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-01-11 17:25:08.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.408][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-01-11 17:25:08.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-01-11 17:25:08.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.414][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-01-11 17:25:08.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-01-11 17:25:08.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-11 17:25:08.450][biodb::testThat]
biodb.INFO [2025-01-11 17:25:08.451][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-01-11 17:25:08.452][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-11 17:25:08.454][biodb::testThat]
biodb.INFO [2025-01-11 17:25:08.468][biodb::testThat]
biodb.INFO [2025-01-11 17:25:08.469][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-01-11 17:25:08.470][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-11 17:25:08.471][biodb::testThat]
biodb.WARN [2025-01-11 17:25:08.550][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2025-01-11 17:25:08.579][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2025-01-11 17:25:08.592][biodb::testThat]
biodb.INFO [2025-01-11 17:25:08.593][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-01-11 17:25:08.595][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-11 17:25:08.596][biodb::testThat]
biodb.TRACE[2025-01-11 17:25:08.643][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-11 17:25:08.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-11 17:25:08.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.650][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-11 17:25:08.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-11 17:25:08.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.657][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-11 17:25:08.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-11 17:25:08.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.662][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-11 17:25:08.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-11 17:25:08.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.706][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-11 17:25:08.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-11 17:25:08.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.711][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-01-11 17:25:08.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-01-11 17:25:08.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.717][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-01-11 17:25:08.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-01-11 17:25:08.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-01-11 17:25:08.722][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-01-11 17:25:08.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-01-11 17:25:08.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-01-11 17:25:08.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-01-11 17:25:08.744][biodb::testThat]
biodb.INFO [2025-01-11 17:25:08.745][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-01-11 17:25:08.746][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-11 17:25:08.748][biodb::testThat]
biodb.INFO [2025-01-11 17:25:08.846][biodb::testThat]
biodb.INFO [2025-01-11 17:25:08.847][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-01-11 17:25:08.849][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-11 17:25:08.851][biodb::testThat]
biodb.INFO [2025-01-11 17:25:08.865][biodb::testThat]
biodb.INFO [2025-01-11 17:25:08.867][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-01-11 17:25:08.868][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-11 17:25:08.869][biodb::testThat]
biodb.INFO [2025-01-11 17:25:08.880][biodb::testThat]
biodb.INFO [2025-01-11 17:25:08.881][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-01-11 17:25:08.883][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-01-11 17:25:08.884][biodb::testThat]
biodb.INFO [2025-01-11 17:25:08.894][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-11 17:25:08.898][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-01-11 17:25:08.899][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-01-11 17:25:08.901][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-11 17:25:08.903][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 17:25:08.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 17:25:08.905][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:08.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:08.907][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:08.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-01-11 17:25:08.945][biodb::testContext]
biodb.INFO [2025-01-11 17:25:08.947][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-11 17:25:08.948][biodb::testContext] Test context - Example long tests
biodb.INFO [2025-01-11 17:25:08.950][biodb::testContext] ********************************************************************************
biodb.INFO [2025-01-11 17:25:08.951][biodb::testContext]
biodb.INFO [2025-01-11 17:25:08.970][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-01-11 17:25:08.974][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-01-11 17:25:09.016][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-11 17:25:09.017][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-01-11 17:25:09.019][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-01-11 17:25:09.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.025][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-01-11 17:25:09.026][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-01-11 17:25:09.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.031][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-01-11 17:25:09.033][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-01-11 17:25:09.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.039][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-01-11 17:25:09.040][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-01-11 17:25:09.042][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-01-11 17:25:09.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.048][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-01-11 17:25:09.049][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-01-11 17:25:09.051][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-01-11 17:25:09.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.056][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-01-11 17:25:09.059][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-01-11 17:25:09.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.064][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-01-11 17:25:09.065][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-01-11 17:25:09.067][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-01-11 17:25:09.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.072][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-01-11 17:25:09.074][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-01-11 17:25:09.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.079][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-01-11 17:25:09.081][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-01-11 17:25:09.083][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-01-11 17:25:09.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.088][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-01-11 17:25:09.090][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-01-11 17:25:09.091][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-01-11 17:25:09.093][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-01-11 17:25:09.094][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-01-11 17:25:09.095][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-01-11 17:25:09.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.101][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-01-11 17:25:09.102][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-01-11 17:25:09.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.107][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-01-11 17:25:09.108][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-01-11 17:25:09.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.114][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-01-11 17:25:09.116][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-01-11 17:25:09.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.119][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[2025-01-11 17:25:09.121][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-01-11 17:25:09.122][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-01-11 17:25:09.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.127][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-01-11 17:25:09.128][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-01-11 17:25:09.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.133][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-01-11 17:25:09.134][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-01-11 17:25:09.139][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-01-11 17:25:09.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.145][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-01-11 17:25:09.146][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-01-11 17:25:09.147][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-01-11 17:25:09.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.153][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-01-11 17:25:09.157][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-11 17:25:09.159][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-01-11 17:25:09.161][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-11 17:25:09.162][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-11 17:25:09.163][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-11 17:25:09.165][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-11 17:25:09.166][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-11 17:25:09.167][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-11 17:25:09.169][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-11 17:25:09.170][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-11 17:25:09.174][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-11 17:25:09.175][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-01-11 17:25:09.177][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-11 17:25:09.178][self$setPropertyValue]
biodb.DEBUG[2025-01-11 17:25:09.179][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-11 17:25:09.181][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-11 17:25:09.181][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-11 17:25:09.181][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-11 17:25:09.181][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-11 17:25:09.181][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-11 17:25:09.182][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-11 17:25:09.183][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-11 17:25:09.184][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-11 17:25:09.186][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-11 17:25:09.187][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-11 17:25:09.189][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-11 17:25:09.190][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-11 17:25:09.191][self$setPropertyValue]
biodb.DEBUG[2025-01-11 17:25:09.192][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-11 17:25:09.194][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-11 17:25:09.195][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-11 17:25:09.196][self$setPropertyValue]
biodb.DEBUG[2025-01-11 17:25:09.198][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-01-11 17:25:09.201][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-11 17:25:09.202][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-01-11 17:25:09.203][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-11 17:25:09.205][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-11 17:25:09.206][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-11 17:25:09.207][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-11 17:25:09.209][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-11 17:25:09.210][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-11 17:25:09.211][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-11 17:25:09.213][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-11 17:25:09.215][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-11 17:25:09.216][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-01-11 17:25:09.218][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-11 17:25:09.219][self$setPropertyValue]
biodb.DEBUG[2025-01-11 17:25:09.220][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-11 17:25:09.222][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-01-11 17:25:09.222][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-01-11 17:25:09.222][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-01-11 17:25:09.222][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-01-11 17:25:09.222][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-01-11 17:25:09.223][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-11 17:25:09.224][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-11 17:25:09.226][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-11 17:25:09.227][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-11 17:25:09.228][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-11 17:25:09.230][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-11 17:25:09.231][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-11 17:25:09.233][self$setPropertyValue]
biodb.DEBUG[2025-01-11 17:25:09.234][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-11 17:25:09.235][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-11 17:25:09.237][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-11 17:25:09.238][self$setPropertyValue]
biodb.DEBUG[2025-01-11 17:25:09.240][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-01-11 17:25:09.242][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-11 17:25:09.243][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-01-11 17:25:09.245][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-11 17:25:09.246][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-11 17:25:09.247][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-11 17:25:09.249][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-11 17:25:09.250][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-11 17:25:09.252][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-11 17:25:09.253][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-01-11 17:25:09.254][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-11 17:25:09.256][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-11 17:25:09.258][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-01-11 17:25:09.259][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-11 17:25:09.260][self$setPropertyValue]
biodb.DEBUG[2025-01-11 17:25:09.262][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-11 17:25:09.263][self$setPropertyValue]
biodb.DEBUG[2025-01-11 17:25:09.264][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-11 17:25:09.266][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-11 17:25:09.267][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-11 17:25:09.268][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-11 17:25:09.269][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-11 17:25:09.271][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-11 17:25:09.272][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-11 17:25:09.273][self$setPropertyValue]
biodb.DEBUG[2025-01-11 17:25:09.275][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-11 17:25:09.276][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-11 17:25:09.277][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-11 17:25:09.278][self$setPropertyValue]
biodb.DEBUG[2025-01-11 17:25:09.280][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-01-11 17:25:09.282][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-01-11 17:25:09.285][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-01-11 17:25:09.286][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-11 17:25:09.288][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-11 17:25:09.289][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-01-11 17:25:09.290][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-01-11 17:25:09.292][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-01-11 17:25:09.293][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-11 17:25:09.294][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-01-11 17:25:09.296][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-11 17:25:09.297][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-01-11 17:25:09.299][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-01-11 17:25:09.300][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-11 17:25:09.301][self$setPropertyValue]
biodb.DEBUG[2025-01-11 17:25:09.303][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-01-11 17:25:09.304][self$setPropertyValue]
biodb.DEBUG[2025-01-11 17:25:09.305][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-01-11 17:25:09.307][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-11 17:25:09.308][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-11 17:25:09.309][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-11 17:25:09.311][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-11 17:25:09.312][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-11 17:25:09.313][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-11 17:25:09.315][self$setPropertyValue]
biodb.DEBUG[2025-01-11 17:25:09.316][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-11 17:25:09.317][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-11 17:25:09.318][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-01-11 17:25:09.320][self$setPropertyValue]
biodb.DEBUG[2025-01-11 17:25:09.322][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-11 17:25:09.324][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.337][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[2025-01-11 17:25:09.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.381][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[2025-01-11 17:25:09.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.388][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[2025-01-11 17:25:09.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.432][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[2025-01-11 17:25:09.433][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-01-11 17:25:09.436][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-01-11 17:25:09.438][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-01-11 17:25:09.440][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-01-11 17:25:09.442][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-01-11 17:25:09.443][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-01-11 17:25:09.445][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-01-11 17:25:09.447][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-01-11 17:25:09.449][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-01-11 17:25:09.451][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-01-11 17:25:09.453][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-01-11 17:25:09.455][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-01-11 17:25:09.456][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-01-11 17:25:09.459][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-01-11 17:25:09.461][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-01-11 17:25:09.462][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-01-11 17:25:09.464][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-01-11 17:25:09.466][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-01-11 17:25:09.468][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-01-11 17:25:09.469][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-01-11 17:25:09.472][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-01-11 17:25:09.473][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-01-11 17:25:09.475][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-01-11 17:25:09.477][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-01-11 17:25:09.479][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-01-11 17:25:09.482][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-01-11 17:25:09.484][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-01-11 17:25:09.486][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-01-11 17:25:09.487][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-01-11 17:25:09.489][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-01-11 17:25:09.491][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-01-11 17:25:09.493][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-01-11 17:25:09.494][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-01-11 17:25:09.496][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-01-11 17:25:09.498][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-01-11 17:25:09.500][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-01-11 17:25:09.502][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-01-11 17:25:09.505][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-01-11 17:25:09.507][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-01-11 17:25:09.509][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-01-11 17:25:09.511][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-01-11 17:25:09.513][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-01-11 17:25:09.514][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-01-11 17:25:09.516][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-01-11 17:25:09.519][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-01-11 17:25:09.520][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-01-11 17:25:09.523][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-01-11 17:25:09.525][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-01-11 17:25:09.527][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-01-11 17:25:09.528][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-01-11 17:25:09.530][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-01-11 17:25:09.532][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-01-11 17:25:09.534][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-01-11 17:25:09.536][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-01-11 17:25:09.537][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-01-11 17:25:09.539][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-01-11 17:25:09.541][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-01-11 17:25:09.543][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-01-11 17:25:09.545][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-01-11 17:25:09.547][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-01-11 17:25:09.549][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-01-11 17:25:09.551][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-01-11 17:25:09.553][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-01-11 17:25:09.555][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-01-11 17:25:09.557][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-01-11 17:25:09.559][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-01-11 17:25:09.561][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-01-11 17:25:09.563][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-01-11 17:25:09.565][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-01-11 17:25:09.566][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-01-11 17:25:09.568][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-01-11 17:25:09.570][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-01-11 17:25:09.572][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-01-11 17:25:09.574][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-01-11 17:25:09.575][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-01-11 17:25:09.577][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-01-11 17:25:09.580][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-01-11 17:25:09.581][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-01-11 17:25:09.583][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-01-11 17:25:09.585][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-01-11 17:25:09.587][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-01-11 17:25:09.589][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-01-11 17:25:09.590][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-01-11 17:25:09.593][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-01-11 17:25:09.596][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-01-11 17:25:09.598][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-01-11 17:25:09.599][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.602][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 17:25:09.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 17:25:09.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 17:25:09.617][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 17:25:09.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 17:25:09.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 17:25:09.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 17:25:09.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 17:25:09.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 17:25:09.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 17:25:09.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 17:25:09.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 17:25:09.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 17:25:09.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 17:25:09.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 17:25:09.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 17:25:09.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.673][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 17:25:09.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 17:25:09.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 17:25:09.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 17:25:09.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 17:25:09.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 17:25:09.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 17:25:09.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 17:25:09.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 17:25:09.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 17:25:09.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 17:25:09.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 17:25:09.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 17:25:09.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 17:25:09.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-01-11 17:25:09.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 17:25:09.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 17:25:09.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.740][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.DEBUG[2025-01-11 17:25:09.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-01-11 17:25:09.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 17:25:09.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 17:25:09.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.749][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[2025-01-11 17:25:09.774][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2025-01-11 17:25:09.786][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2025-01-11 17:25:09.789][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-01-11 17:25:09.790][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2025-01-11 17:25:09.791][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-01-11 17:25:09.793][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-01-11 17:25:09.794][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2025-01-11 17:25:09.795][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2025-01-11 17:25:09.797][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-01-11 17:25:09.798][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-01-11 17:25:09.799][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2025-01-11 17:25:09.801][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-01-11 17:25:09.802][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-01-11 17:25:09.804][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2025-01-11 17:25:09.805][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-01-11 17:25:09.807][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2025-01-11 17:25:09.807][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2025-01-11 17:25:09.807][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2025-01-11 17:25:09.807][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2025-01-11 17:25:09.807][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2025-01-11 17:25:09.807][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2025-01-11 17:25:09.807][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2025-01-11 17:25:09.810][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-01-11 17:25:09.811][self$setPropertyValue]
biodb.DEBUG[2025-01-11 17:25:09.812][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-01-11 17:25:09.814][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-11 17:25:09.815][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-11 17:25:09.816][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-01-11 17:25:09.817][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-01-11 17:25:09.819][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-01-11 17:25:09.820][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-01-11 17:25:09.821][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-01-11 17:25:09.821][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2025-01-11 17:25:09.821][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2025-01-11 17:25:09.821][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2025-01-11 17:25:09.822][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-01-11 17:25:09.824][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-01-11 17:25:09.825][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-01-11 17:25:09.827][self$setPropertyValue]
biodb.DEBUG[2025-01-11 17:25:09.829][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2025-01-11 17:25:09.835][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2025-01-11 17:25:09.836][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2025-01-11 17:25:09.838][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2025-01-11 17:25:09.842][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2025-01-11 17:25:09.844][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-11 17:25:09.846][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-01-11 17:25:09.847][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-01-11 17:25:09.849][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-01-11 17:25:09.851][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2025-01-11 17:25:09.852][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2025-01-11 17:25:09.853][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-01-11 17:25:09.855][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2025-01-11 17:25:09.856][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2025-01-11 17:25:09.858][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-01-11 17:25:09.859][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-01-11 17:25:09.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-01-11 17:25:09.862][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-01-11 17:25:09.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-01-11 17:25:09.864][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-01-11 17:25:09.865][FUN] Functions in observer 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 
1241.68  382.21 4775.62

'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) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* 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' ...
** 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   -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   -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   -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   -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)