Back to Long Tests report for BioC 3.22 |
This page was generated on 2025-08-09 23:55 -0400 (Sat, 09 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
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 8/29 | Hostname | OS / Arch | CHECK | |||||||
Pierrick Roger
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | ERROR | |||||||
palomino8 | Windows Server 2022 Datacenter / x64 | ERROR | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ||||||||
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. |
Package: biodbNci |
Version: 1.13.1 |
Command: F:\biocbuild\bbs-3.22-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_1.13.1.tar.gz |
StartedAt: 2025-08-09 16:02:49 -0400 (Sat, 09 Aug 2025) |
EndedAt: 2025-08-09 16:04:28 -0400 (Sat, 09 Aug 2025) |
EllapsedTime: 98.5 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: biodbNci.Rcheck |
Warnings: NA |
biodbNci.Rcheck/tests/testthat.Rout.fail
R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # Script needed to run testthat automatically from ‘R CMD check’. See > # testthat::test_dir documentation. > library(testthat) > library(biodbNci) Warning message: In fun(libname, pkgname) : Package 'biodbNci' is deprecated and will be removed from Bioconductor version 3.23 > Sys.setenv(TESTTHAT_REPORTER="summary") > Sys.setenv(BIODB_LOG_DST="console") > test_check("biodbNci") biodb.INFO [2025-08-09 16:04:24.342][biodb::testContext] biodb.INFO [2025-08-09 16:04:24.345][biodb::testContext] ******************************************************************************** biodb.INFO [2025-08-09 16:04:24.346][biodb::testContext] Test context - Generic long tests biodb.INFO [2025-08-09 16:04:24.347][biodb::testContext] ******************************************************************************** biodb.INFO [2025-08-09 16:04:24.348][biodb::testContext] biodb.INFO [2025-08-09 16:04:24.354][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1. biodb.DEBUG[2025-08-09 16:04:24.357][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.22-bioc/R/library/biodb/definitions.yml". biodb.DEBUG[2025-08-09 16:04:24.364][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-08-09 16:04:24.366][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2025-08-09 16:04:24.367][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2025-08-09 16:04:24.368][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:24.371][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2025-08-09 16:04:24.387][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2025-08-09 16:04:24.388][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:24.391][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2025-08-09 16:04:24.392][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2025-08-09 16:04:24.394][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:24.397][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2025-08-09 16:04:24.398][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2025-08-09 16:04:24.399][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2025-08-09 16:04:24.401][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:24.404][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2025-08-09 16:04:24.405][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2025-08-09 16:04:24.406][self$set] Set key cache.system to TRUE. biodb.DEBUG[2025-08-09 16:04:24.407][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:24.411][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2025-08-09 16:04:24.412][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2025-08-09 16:04:24.413][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:24.417][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2025-08-09 16:04:24.418][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2025-08-09 16:04:24.419][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2025-08-09 16:04:24.420][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:24.423][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2025-08-09 16:04:24.425][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2025-08-09 16:04:24.426][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:24.429][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2025-08-09 16:04:24.430][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2025-08-09 16:04:24.432][self$set] Set key force.locale to TRUE. biodb.DEBUG[2025-08-09 16:04:24.433][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:24.436][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2025-08-09 16:04:24.437][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2025-08-09 16:04:24.438][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2025-08-09 16:04:24.440][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2025-08-09 16:04:24.441][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2025-08-09 16:04:24.442][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2025-08-09 16:04:24.443][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:24.447][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2025-08-09 16:04:24.448][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2025-08-09 16:04:24.449][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:24.452][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2025-08-09 16:04:24.454][self$set] Set key entries.sep to "|". biodb.DEBUG[2025-08-09 16:04:24.455][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:24.464][self$getConfig()$define] Define config key offline. biodb.DEBUG[2025-08-09 16:04:24.465][self$set] Set key offline to FALSE. biodb.DEBUG[2025-08-09 16:04:24.466][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:24.469][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2025-08-09 16:04:24.470][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2025-08-09 16:04:24.472][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2025-08-09 16:04:24.473][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:24.476][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2025-08-09 16:04:24.477][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2025-08-09 16:04:24.481][self$set] Set key svn.binary.path to "". biodb.DEBUG[2025-08-09 16:04:24.482][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:24.485][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2025-08-09 16:04:24.487][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2025-08-09 16:04:24.488][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2025-08-09 16:04:24.489][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:24.494][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2025-08-09 16:04:24.521][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-08-09 16:04:24.535][self$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[2025-08-09 16:04:24.536][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-09 16:04:24.538][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-09 16:04:24.539][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-08-09 16:04:24.540][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-08-09 16:04:24.541][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-08-09 16:04:24.542][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-09 16:04:24.544][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-08-09 16:04:24.545][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-09 16:04:24.546][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-08-09 16:04:24.547][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2025-08-09 16:04:24.549][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-09 16:04:24.550][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-08-09 16:04:24.551][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-08-09 16:04:24.552][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-08-09 16:04:24.552][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-08-09 16:04:24.552][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-08-09 16:04:24.552][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-08-09 16:04:24.552][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-08-09 16:04:24.554][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-08-09 16:04:24.555][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:04:24.556][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:04:24.557][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-09 16:04:24.558][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:04:24.559][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:04:24.560][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-09 16:04:24.562][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-08-09 16:04:24.563][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-09 16:04:24.564][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-09 16:04:24.565][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-08-09 16:04:24.566][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-09 16:04:24.568][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2025-08-09 16:04:24.570][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-08-09 16:04:24.571][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2025-08-09 16:04:24.572][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-09 16:04:24.573][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-09 16:04:24.574][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-08-09 16:04:24.576][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-08-09 16:04:24.577][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-08-09 16:04:24.578][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-09 16:04:24.579][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-08-09 16:04:24.580][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-09 16:04:24.582][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-08-09 16:04:24.583][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2025-08-09 16:04:24.584][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-09 16:04:24.585][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-08-09 16:04:24.586][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-08-09 16:04:24.588][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-08-09 16:04:24.588][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-08-09 16:04:24.588][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-08-09 16:04:24.588][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-08-09 16:04:24.588][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-08-09 16:04:24.589][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-08-09 16:04:24.590][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:04:24.591][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:04:24.592][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-09 16:04:24.593][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:04:24.594][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:04:24.596][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-09 16:04:24.597][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-08-09 16:04:24.598][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-09 16:04:24.599][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-09 16:04:24.600][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-08-09 16:04:24.601][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-09 16:04:24.603][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2025-08-09 16:04:24.605][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-08-09 16:04:24.606][self$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[2025-08-09 16:04:24.607][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-09 16:04:24.608][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-09 16:04:24.610][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-08-09 16:04:24.611][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-08-09 16:04:24.612][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-08-09 16:04:24.613][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-09 16:04:24.614][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-08-09 16:04:24.616][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-09 16:04:24.617][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-08-09 16:04:24.618][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2025-08-09 16:04:24.619][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-09 16:04:24.620][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-08-09 16:04:24.622][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-08-09 16:04:24.623][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>". biodb.DEBUG[2025-08-09 16:04:24.624][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-08-09 16:04:24.625][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:04:24.626][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:04:24.627][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-09 16:04:24.629][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:04:24.630][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:04:24.631][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-09 16:04:24.632][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-08-09 16:04:24.633][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-09 16:04:24.634][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-09 16:04:24.636][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-08-09 16:04:24.637][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-09 16:04:24.638][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2025-08-09 16:04:24.640][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-08-09 16:04:24.641][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2025-08-09 16:04:24.643][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-09 16:04:24.649][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-09 16:04:24.650][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-08-09 16:04:24.651][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-08-09 16:04:24.653][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-08-09 16:04:24.654][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-09 16:04:24.655][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-08-09 16:04:24.656][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-09 16:04:24.657][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-08-09 16:04:24.659][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2025-08-09 16:04:24.660][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-09 16:04:24.661][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-08-09 16:04:24.662][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-08-09 16:04:24.664][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>". biodb.DEBUG[2025-08-09 16:04:24.665][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-08-09 16:04:24.666][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:04:24.667][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:04:24.668][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-09 16:04:24.669][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:04:24.671][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:04:24.672][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-09 16:04:24.673][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-08-09 16:04:24.674][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-09 16:04:24.675][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-09 16:04:24.677][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-08-09 16:04:24.678][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-09 16:04:24.681][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-08-09 16:04:24.682][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.683][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[2025-08-09 16:04:24.684][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:24.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:24.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.689][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[2025-08-09 16:04:24.690][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:24.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:24.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:24.695][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:24.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:24.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:24.701][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:24.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:24.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:24.706][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:24.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:24.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:24.712][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:24.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:24.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:24.717][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:24.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:24.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:24.723][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:24.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:24.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:24.728][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:24.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:24.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.732][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[2025-08-09 16:04:24.734][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:24.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:24.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.740][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[2025-08-09 16:04:24.743][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:24.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:24.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.749][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[2025-08-09 16:04:24.750][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:24.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:24.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:24.755][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:24.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:24.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:24.761][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:24.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:24.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:24.766][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:24.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:24.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:24.772][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:24.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:24.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:24.777][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2025-08-09 16:04:24.781][self$getEntryFields()$define] Define field description. biodb.DEBUG[2025-08-09 16:04:24.783][self$getEntryFields()$define] Define field name. biodb.DEBUG[2025-08-09 16:04:24.784][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2025-08-09 16:04:24.786][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2025-08-09 16:04:24.787][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2025-08-09 16:04:24.789][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2025-08-09 16:04:24.790][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2025-08-09 16:04:24.792][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2025-08-09 16:04:24.793][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2025-08-09 16:04:24.795][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2025-08-09 16:04:24.797][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2025-08-09 16:04:24.798][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2025-08-09 16:04:24.800][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2025-08-09 16:04:24.801][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2025-08-09 16:04:24.803][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2025-08-09 16:04:24.804][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2025-08-09 16:04:24.806][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2025-08-09 16:04:24.807][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2025-08-09 16:04:24.809][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2025-08-09 16:04:24.811][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2025-08-09 16:04:24.812][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2025-08-09 16:04:24.814][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2025-08-09 16:04:24.815][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2025-08-09 16:04:24.817][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2025-08-09 16:04:24.818][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2025-08-09 16:04:24.820][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2025-08-09 16:04:24.821][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2025-08-09 16:04:24.823][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2025-08-09 16:04:24.825][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2025-08-09 16:04:24.826][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2025-08-09 16:04:24.828][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2025-08-09 16:04:24.829][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2025-08-09 16:04:24.831][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2025-08-09 16:04:24.832][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2025-08-09 16:04:24.834][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2025-08-09 16:04:24.836][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2025-08-09 16:04:24.837][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2025-08-09 16:04:24.839][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2025-08-09 16:04:24.840][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2025-08-09 16:04:24.842][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2025-08-09 16:04:24.844][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2025-08-09 16:04:24.845][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2025-08-09 16:04:24.847][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2025-08-09 16:04:24.854][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2025-08-09 16:04:24.855][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2025-08-09 16:04:24.857][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2025-08-09 16:04:24.858][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2025-08-09 16:04:24.860][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2025-08-09 16:04:24.862][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2025-08-09 16:04:24.863][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2025-08-09 16:04:24.865][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2025-08-09 16:04:24.866][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2025-08-09 16:04:24.868][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2025-08-09 16:04:24.869][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2025-08-09 16:04:24.871][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2025-08-09 16:04:24.873][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2025-08-09 16:04:24.874][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2025-08-09 16:04:24.876][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2025-08-09 16:04:24.877][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2025-08-09 16:04:24.879][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2025-08-09 16:04:24.881][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2025-08-09 16:04:24.882][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2025-08-09 16:04:24.884][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2025-08-09 16:04:24.885][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2025-08-09 16:04:24.887][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2025-08-09 16:04:24.888][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2025-08-09 16:04:24.890][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2025-08-09 16:04:24.891][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2025-08-09 16:04:24.893][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2025-08-09 16:04:24.894][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2025-08-09 16:04:24.896][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2025-08-09 16:04:24.898][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2025-08-09 16:04:24.899][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2025-08-09 16:04:24.901][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2025-08-09 16:04:24.902][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2025-08-09 16:04:24.904][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2025-08-09 16:04:24.905][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2025-08-09 16:04:24.907][self$getEntryFields()$define] Define field products. biodb.DEBUG[2025-08-09 16:04:24.909][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2025-08-09 16:04:24.910][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2025-08-09 16:04:24.912][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2025-08-09 16:04:24.913][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2025-08-09 16:04:24.948][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2025-08-09 16:04:24.950][initialize] This is biodb version 1.17.1. biodb.DEBUG[2025-08-09 16:04:24.953][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-08-09 16:04:24.954][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:24.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:24.956][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.958][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[2025-08-09 16:04:24.962][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:24.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:24.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:24.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:24.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:24.970][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:24.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:24.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:24.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:24.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:24.977][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:24.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:24.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:24.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:24.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:24.985][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:24.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:24.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:24.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:24.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:24.993][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:24.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:24.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:24.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:24.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:24.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:24.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:25.000][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:25.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:25.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:25.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:25.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:25.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:25.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:25.008][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:25.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:25.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:25.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:25.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:25.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:25.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:25.015][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:25.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:25.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:25.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:25.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:25.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:25.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:25.023][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:25.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:25.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:25.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:25.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:25.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:25.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:25.031][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:25.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:25.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:25.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:25.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:25.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:25.037][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[2025-08-09 16:04:25.038][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:25.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:25.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:25.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:25.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:25.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:25.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:25.046][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:25.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:25.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:25.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:25.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:25.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:25.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:25.053][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:25.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:25.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:25.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:25.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:25.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:25.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:25.061][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:25.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:25.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:25.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:25.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:25.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:25.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:25.074][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:25.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:25.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:25.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:25.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:25.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:25.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:25.081][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:25.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:25.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:25.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:25.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:25.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:25.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:25.091][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml". biodb.DEBUG[2025-08-09 16:04:25.100][self$getDbsInfo()$define] Define connector nci.cactus. biodb.DEBUG[2025-08-09 16:04:25.103][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-08-09 16:04:25.104][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.". biodb.DEBUG[2025-08-09 16:04:25.105][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-09 16:04:25.106][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-09 16:04:25.108][self$setPropertyValue] Setting property "downloadable" to "TRUE". biodb.DEBUG[2025-08-09 16:04:25.109][self$setPropertyValue] Setting property "dwnld.ext" to "gz". biodb.DEBUG[2025-08-09 16:04:25.110][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2025-08-09 16:04:25.111][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-09 16:04:25.112][self$setPropertyValue] Setting property "entry.content.type" to "sdf". biodb.DEBUG[2025-08-09 16:04:25.114][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-09 16:04:25.115][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-08-09 16:04:25.116][self$setPropertyValue] Setting property "name" to "NCI CACTUS". biodb.DEBUG[2025-08-09 16:04:25.117][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-09 16:04:25.119][self$setPropertyValue] Setting property "parsing.expr" to "NSC". biodb.DEBUG[2025-08-09 16:04:25.119][self$setPropertyValue] Setting property "parsing.expr" to "DTP names". biodb.DEBUG[2025-08-09 16:04:25.119][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI". biodb.DEBUG[2025-08-09 16:04:25.119][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")". biodb.DEBUG[2025-08-09 16:04:25.119][self$setPropertyValue] Setting property "parsing.expr" to "Formula". biodb.DEBUG[2025-08-09 16:04:25.119][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight". biodb.DEBUG[2025-08-09 16:04:25.119][self$setPropertyValue] Setting property "parsing.expr" to "CAS". biodb.DEBUG[2025-08-09 16:04:25.120][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2025-08-09 16:04:25.121][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>". biodb.DEBUG[2025-08-09 16:04:25.122][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2025-08-09 16:04:25.123][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:04:25.125][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:04:25.126][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-09 16:04:25.127][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:04:25.128][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:04:25.129][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-09 16:04:25.130][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/". biodb.DEBUG[2025-08-09 16:04:25.130][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/". biodb.DEBUG[2025-08-09 16:04:25.130][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/". biodb.DEBUG[2025-08-09 16:04:25.130][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz". biodb.DEBUG[2025-08-09 16:04:25.132][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-09 16:04:25.133][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-09 16:04:25.134][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2025-08-09 16:04:25.135][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-09 16:04:25.141][self$getEntryFields()$define] Define field nci.cactus.id. biodb.DEBUG[2025-08-09 16:04:25.160][super$initialize] Initialize connector nci.cactus. biodb.DEBUG[2025-08-09 16:04:25.187][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus . biodb.INFO [2025-08-09 16:04:25.197][biodb::testThat] biodb.INFO [2025-08-09 16:04:25.199][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value "). biodb.INFO [2025-08-09 16:04:25.200][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-09 16:04:25.201][biodb::testThat] biodb.TRACE[2025-08-09 16:04:25.206][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf". biodb.DEBUG[2025-08-09 16:04:25.208][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s). biodb.DEBUG[2025-08-09 16:04:25.211][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries. biodb.DEBUG[2025-08-09 16:04:25.218][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-08-09 16:04:25.219][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:25.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:25.236][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:25.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:25.238][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:25.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-08-09 16:04:25.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:25.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:25.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.259][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:25.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:25.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.274][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.277][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:04:25.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:04:25.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.290][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.313][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:04:25.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:04:25.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.317][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.319][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:04:25.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:04:25.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.322][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:04:25.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:04:25.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.327][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.329][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:04:25.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:04:25.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.333][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.334][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:04:25.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:04:25.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.338][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.340][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:04:25.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:04:25.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.343][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.344][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:04:25.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:04:25.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.348][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.350][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:04:25.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:04:25.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.354][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.355][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:04:25.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:04:25.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.358][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:25.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:25.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.363][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.365][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:04:25.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:04:25.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.368][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:25.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:25.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.373][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:25.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:25.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.378][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:25.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:25.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.383][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:25.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:25.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.419][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:25.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:25.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.424][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:25.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:25.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.429][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-08-09 16:04:25.430][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674. biodb.TRACE[2025-08-09 16:04:25.433][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-08-09 16:04:25.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-08-09 16:04:25.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.437][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.438][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-08-09 16:04:25.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-08-09 16:04:25.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.442][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.443][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2025-08-09 16:04:25.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2025-08-09 16:04:25.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.448][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2025-08-09 16:04:25.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2025-08-09 16:04:25.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.451][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:25.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:25.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.458][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.472][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:04:25.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:04:25.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.475][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:25.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:25.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.486][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:25.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:25.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.491][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.492][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:25.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:25.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.496][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:25.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:25.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.502][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:25.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:25.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.507][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:25.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:25.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.512][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.513][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:04:25.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:04:25.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.517][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.518][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:04:25.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:04:25.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.522][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.523][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:04:25.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:04:25.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.526][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:25.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:25.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.540][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:25.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:25.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.545][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:25.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:25.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.550][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.551][ef$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:25.552][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:25.553][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.554][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:25.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:25.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.559][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.575][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:04:25.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:04:25.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.579][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.580][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:04:25.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:04:25.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.584][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.585][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:04:25.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:04:25.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.589][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.590][ef$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:04:25.591][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:04:25.592][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.593][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.595][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:04:25.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:04:25.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.598][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.609][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:04:25.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:04:25.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.613][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.614][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:04:25.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:04:25.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.618][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.619][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:04:25.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:04:25.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.623][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.624][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:04:25.625][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:04:25.626][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.627][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.629][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:04:25.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:04:25.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.632][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.643][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:04:25.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:04:25.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.647][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.648][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:04:25.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:04:25.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.651][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.653][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:04:25.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:04:25.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.656][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.658][ef$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:04:25.659][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:04:25.660][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.661][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.662][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:04:25.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:04:25.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.666][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.676][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:04:25.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:04:25.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.680][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.681][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:04:25.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:04:25.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.685][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.686][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:04:25.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:04:25.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.690][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.691][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:04:25.692][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:04:25.694][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.695][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.696][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:04:25.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:04:25.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.700][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.710][ef$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:25.712][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:25.713][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.714][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.720][ef$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:04:25.722][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:04:25.723][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.724][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.767][ef$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:04:25.769][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:04:25.770][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.772][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.778][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:04:25.780][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:04:25.781][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.782][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.789][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:04:25.790][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:04:25.791][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.792][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.811][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf". biodb.DEBUG[2025-08-09 16:04:25.840][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s). biodb.DEBUG[2025-08-09 16:04:25.842][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries. biodb.DEBUG[2025-08-09 16:04:25.844][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-08-09 16:04:25.845][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:25.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:25.853][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:25.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:25.855][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:25.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-08-09 16:04:25.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:25.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:25.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.870][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:25.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:25.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.874][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.896][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-08-09 16:04:25.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-08-09 16:04:25.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.900][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.901][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-08-09 16:04:25.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-08-09 16:04:25.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.905][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.907][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:04:25.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:04:25.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.910][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.911][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:04:25.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:04:25.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.915][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.917][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:04:25.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:04:25.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.920][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.922][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:04:25.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:04:25.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.925][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.927][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:04:25.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:04:25.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.930][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.932][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:04:25.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:04:25.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.935][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.937][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:04:25.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:04:25.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.940][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.942][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:04:25.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:04:25.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.945][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.946][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:04:25.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:04:25.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.950][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.951][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:04:25.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:04:25.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.955][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.956][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:04:25.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:04:25.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.960][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.962][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:04:25.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:04:25.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.965][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.967][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:04:25.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:04:25.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.970][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.972][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:04:25.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:04:25.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.976][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.977][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:04:25.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:04:25.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.981][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.983][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:04:25.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:04:25.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.986][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.987][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:04:25.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:04:25.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.991][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:25.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:25.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:25.996][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:25.997][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:04:25.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:04:25.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.001][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:26.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:26.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.005][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:26.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:26.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.010][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:26.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:26.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:26.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:26.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.020][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:26.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:26.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.025][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:26.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:26.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.030][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-08-09 16:04:26.031][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690. biodb.TRACE[2025-08-09 16:04:26.053][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-08-09 16:04:26.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-08-09 16:04:26.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.057][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.059][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-08-09 16:04:26.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-08-09 16:04:26.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.062][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.063][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2025-08-09 16:04:26.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2025-08-09 16:04:26.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.067][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.068][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2025-08-09 16:04:26.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2025-08-09 16:04:26.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.072][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:26.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:26.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.078][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.085][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:04:26.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:04:26.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.088][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.095][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:26.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:26.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.099][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:26.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:26.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.103][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:26.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:26.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.108][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:26.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:26.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.115][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:26.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:26.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.121][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:26.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:26.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.126][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.127][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:04:26.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:04:26.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.131][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.132][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:04:26.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:04:26.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.136][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.137][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:04:26.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:04:26.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.141][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:26.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:26.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.162][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:26.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:26.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.167][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:26.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:26.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.172][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.173][ef$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:26.175][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:26.176][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.177][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:26.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:26.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.182][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.197][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-08-09 16:04:26.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-08-09 16:04:26.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.201][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.202][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-08-09 16:04:26.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-08-09 16:04:26.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.205][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.207][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-08-09 16:04:26.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-08-09 16:04:26.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.210][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.211][ef$get] Asked field names are: cas.id. biodb.TRACE[2025-08-09 16:04:26.213][ef$get] Realnames of fields are: cas.id. biodb.TRACE[2025-08-09 16:04:26.214][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.215][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.216][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-08-09 16:04:26.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-08-09 16:04:26.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.220][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.231][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:04:26.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:04:26.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.234][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.236][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:04:26.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:04:26.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.239][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.240][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:04:26.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:04:26.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.244][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.245][ef$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:04:26.246][ef$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:04:26.248][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.249][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.250][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:04:26.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:04:26.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.253][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.264][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:04:26.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:04:26.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.268][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.269][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:04:26.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:04:26.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.272][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.274][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:04:26.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:04:26.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.277][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.279][ef$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:04:26.280][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:04:26.281][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.282][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.283][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:04:26.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:04:26.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.287][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.298][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:04:26.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:04:26.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.302][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.303][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:04:26.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:04:26.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.306][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.308][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:04:26.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:04:26.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.311][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.312][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:04:26.314][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:04:26.315][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.316][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.317][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:04:26.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:04:26.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.321][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.332][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:04:26.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:04:26.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.335][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.337][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:04:26.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:04:26.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.340][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.341][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:04:26.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:04:26.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.345][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.346][ef$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:04:26.348][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:04:26.349][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.350][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.351][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:04:26.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:04:26.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.359][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.370][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:04:26.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:04:26.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.374][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.375][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:04:26.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:04:26.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.379][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.380][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:04:26.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:04:26.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.383][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.385][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:04:26.386][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:04:26.387][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.388][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.390][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:04:26.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:04:26.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.393][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.404][ef$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:04:26.405][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:04:26.407][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.408][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.414][ef$get] Asked field names are: cas.id. biodb.TRACE[2025-08-09 16:04:26.415][ef$get] Realnames of fields are: cas.id. biodb.TRACE[2025-08-09 16:04:26.417][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.418][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.424][ef$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:04:26.425][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:04:26.426][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.428][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.434][ef$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:04:26.435][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:04:26.436][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.437][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.444][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:04:26.445][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:04:26.446][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.447][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.454][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:04:26.455][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:04:26.456][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.457][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:04:26.464][ef$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:04:26.465][ef$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:04:26.466][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:04:26.467][ef$get] fields variable is a list. biodb.INFO [2025-08-09 16:04:26.479][biodb::testThat] biodb.INFO [2025-08-09 16:04:26.480][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. "). biodb.INFO [2025-08-09 16:04:26.481][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-09 16:04:26.482][biodb::testThat] biodb.DEBUG[2025-08-09 16:04:26.485][private$loadEntries] Creating entries from ids [2]: "749674, 750690". biodb.DEBUG[2025-08-09 16:04:26.505][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)... biodb.DEBUG[2025-08-09 16:04:26.508][self$isDownloaded] Database nci.cactus has already been downloaded. biodb.DEBUG[2025-08-09 16:04:26.539][self$isDownloaded] Database nci.cactus has already been downloaded. biodb.INFO [2025-08-09 16:04:26.541][self$download] Extract whole database of nci.cactus. biodb.INFO [2025-08-09 16:04:26.542][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database.... biodb.INFO [2025-08-09 16:04:26.584][biodb::testThat] biodb.INFO [2025-08-09 16:04:26.585][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field "). biodb.INFO [2025-08-09 16:04:26.587][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-09 16:04:26.588][biodb::testThat] biodb.INFO [2025-08-09 16:04:26.596][biodb::testThat] biodb.INFO [2025-08-09 16:04:26.597][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. "). biodb.INFO [2025-08-09 16:04:26.599][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-09 16:04:26.600][biodb::testThat] biodb.WARN [2025-08-09 16:04:26.617][self$searchForEntries] This database is not searchable by field "name". biodb.WARN [2025-08-09 16:04:26.634][self$searchForEntries] This database is not searchable by field "name". biodb.INFO [2025-08-09 16:04:26.646][biodb::testThat] biodb.INFO [2025-08-09 16:04:26.647][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. "). biodb.INFO [2025-08-09 16:04:26.648][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-09 16:04:26.650][biodb::testThat] biodb.DEBUG[2025-08-09 16:04:26.673][private$loadEntries] Creating entries from ids [1]: "749674". biodb.DEBUG[2025-08-09 16:04:26.712][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)... biodb.DEBUG[2025-08-09 16:04:26.714][self$isDownloaded] Database nci.cactus has already been downloaded. biodb.DEBUG[2025-08-09 16:04:26.716][self$isDownloaded] Database nci.cactus has already been downloaded. biodb.INFO [2025-08-09 16:04:26.717][self$download] Extract whole database of nci.cactus. biodb.INFO [2025-08-09 16:04:26.729][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database.... biodb.INFO [2025-08-09 16:04:26.757][biodb::testThat] biodb.INFO [2025-08-09 16:04:26.763][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. "). biodb.INFO [2025-08-09 16:04:26.764][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-09 16:04:26.766][biodb::testThat] biodb.INFO [2025-08-09 16:04:26.776][biodb::testThat] biodb.INFO [2025-08-09 16:04:26.777][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. "). biodb.INFO [2025-08-09 16:04:26.778][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-09 16:04:26.780][biodb::testThat] biodb.INFO [2025-08-09 16:04:26.790][biodb::testThat] biodb.INFO [2025-08-09 16:04:26.792][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. "). biodb.INFO [2025-08-09 16:04:26.793][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-09 16:04:26.794][biodb::testThat] biodb.INFO [2025-08-09 16:04:26.803][biodb::testThat] biodb.INFO [2025-08-09 16:04:26.804][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. "). biodb.INFO [2025-08-09 16:04:26.806][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-09 16:04:26.807][biodb::testThat] biodb.INFO [2025-08-09 16:04:26.815][biodb$terminate] Closing BiodbMain instance... biodb.INFO [2025-08-09 16:04:26.817][self$deleteConn] Connector "nci.cactus" deleted. biodb.DEBUG[2025-08-09 16:04:26.818][notifyObservers] Notify observers for terminate. biodb.DEBUG[2025-08-09 16:04:26.819][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:26.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:26.821][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:26.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:26.823][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:26.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.INFO [2025-08-09 16:04:26.835][biodb::testContext] biodb.INFO [2025-08-09 16:04:26.836][biodb::testContext] ******************************************************************************** biodb.INFO [2025-08-09 16:04:26.837][biodb::testContext] Test context - Example long tests biodb.INFO [2025-08-09 16:04:26.839][biodb::testContext] ******************************************************************************** biodb.INFO [2025-08-09 16:04:26.840][biodb::testContext] biodb.INFO [2025-08-09 16:04:26.843][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1. biodb.DEBUG[2025-08-09 16:04:26.845][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.22-bioc/R/library/biodb/definitions.yml". biodb.DEBUG[2025-08-09 16:04:26.850][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-08-09 16:04:26.852][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2025-08-09 16:04:26.853][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2025-08-09 16:04:26.854][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:26.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:26.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:26.857][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2025-08-09 16:04:26.859][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2025-08-09 16:04:26.860][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:26.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:26.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:26.863][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2025-08-09 16:04:26.864][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2025-08-09 16:04:26.866][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:26.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:26.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:26.869][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2025-08-09 16:04:26.870][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2025-08-09 16:04:26.871][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2025-08-09 16:04:26.873][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:26.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:26.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:26.876][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2025-08-09 16:04:26.877][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2025-08-09 16:04:26.878][self$set] Set key cache.system to TRUE. biodb.DEBUG[2025-08-09 16:04:26.879][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:26.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:26.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:26.883][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2025-08-09 16:04:26.884][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2025-08-09 16:04:26.885][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:26.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:26.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:26.889][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2025-08-09 16:04:26.890][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2025-08-09 16:04:26.891][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2025-08-09 16:04:26.892][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:26.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:26.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:26.895][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2025-08-09 16:04:26.897][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2025-08-09 16:04:26.898][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:26.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:26.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:26.901][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2025-08-09 16:04:26.902][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2025-08-09 16:04:26.904][self$set] Set key force.locale to TRUE. biodb.DEBUG[2025-08-09 16:04:26.905][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:26.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:26.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:26.908][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2025-08-09 16:04:26.909][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2025-08-09 16:04:26.911][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2025-08-09 16:04:26.912][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2025-08-09 16:04:26.913][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2025-08-09 16:04:26.914][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2025-08-09 16:04:26.915][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:26.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:26.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:26.919][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2025-08-09 16:04:26.925][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2025-08-09 16:04:26.926][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:26.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:26.928][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[2025-08-09 16:04:26.930][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2025-08-09 16:04:26.931][self$set] Set key entries.sep to "|". biodb.DEBUG[2025-08-09 16:04:26.932][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:26.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:26.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:26.935][self$getConfig()$define] Define config key offline. biodb.DEBUG[2025-08-09 16:04:26.936][self$set] Set key offline to FALSE. biodb.DEBUG[2025-08-09 16:04:26.938][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:26.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:26.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:26.941][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2025-08-09 16:04:26.942][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2025-08-09 16:04:26.943][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2025-08-09 16:04:26.944][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:26.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:26.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:26.948][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2025-08-09 16:04:26.949][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2025-08-09 16:04:26.953][self$set] Set key svn.binary.path to "". biodb.DEBUG[2025-08-09 16:04:26.954][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:26.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:26.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:26.957][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2025-08-09 16:04:26.959][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2025-08-09 16:04:26.960][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2025-08-09 16:04:26.961][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:26.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:26.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:26.965][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2025-08-09 16:04:26.967][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-08-09 16:04:26.968][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2025-08-09 16:04:26.969][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-09 16:04:26.970][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-09 16:04:26.971][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-08-09 16:04:26.973][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-08-09 16:04:26.974][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-08-09 16:04:26.975][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-09 16:04:26.976][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-08-09 16:04:26.978][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-09 16:04:26.979][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-08-09 16:04:26.980][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2025-08-09 16:04:26.981][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-09 16:04:26.982][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-08-09 16:04:26.984][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-08-09 16:04:26.985][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-08-09 16:04:26.985][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-08-09 16:04:26.985][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-08-09 16:04:26.985][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-08-09 16:04:26.985][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-08-09 16:04:26.986][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-08-09 16:04:26.987][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:04:26.988][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:04:26.990][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-09 16:04:26.991][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:04:26.992][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:04:26.993][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-09 16:04:26.994][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-08-09 16:04:26.995][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-09 16:04:26.997][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-09 16:04:26.998][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-08-09 16:04:26.999][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-09 16:04:27.000][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2025-08-09 16:04:27.002][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-08-09 16:04:27.004][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2025-08-09 16:04:27.005][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-09 16:04:27.006][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-09 16:04:27.007][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-08-09 16:04:27.008][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-08-09 16:04:27.010][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-08-09 16:04:27.011][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-09 16:04:27.012][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-08-09 16:04:27.013][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-09 16:04:27.015][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-08-09 16:04:27.016][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2025-08-09 16:04:27.017][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-09 16:04:27.018][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-08-09 16:04:27.019][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-08-09 16:04:27.021][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-08-09 16:04:27.021][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-08-09 16:04:27.021][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-08-09 16:04:27.021][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-08-09 16:04:27.021][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-08-09 16:04:27.022][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-08-09 16:04:27.023][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:04:27.024][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:04:27.025][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-09 16:04:27.027][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:04:27.028][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:04:27.029][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-09 16:04:27.030][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-08-09 16:04:27.031][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-09 16:04:27.032][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-09 16:04:27.033][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-08-09 16:04:27.035][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-09 16:04:27.036][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2025-08-09 16:04:27.038][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-08-09 16:04:27.039][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2025-08-09 16:04:27.040][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-09 16:04:27.042][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-09 16:04:27.043][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-08-09 16:04:27.044][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-08-09 16:04:27.045][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-08-09 16:04:27.047][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-09 16:04:27.048][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-08-09 16:04:27.049][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-09 16:04:27.050][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-08-09 16:04:27.051][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2025-08-09 16:04:27.053][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-09 16:04:27.054][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-08-09 16:04:27.055][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-08-09 16:04:27.056][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>". biodb.DEBUG[2025-08-09 16:04:27.057][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-08-09 16:04:27.059][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:04:27.060][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:04:27.061][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-09 16:04:27.062][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:04:27.063][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:04:27.064][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-09 16:04:27.066][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-08-09 16:04:27.067][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-09 16:04:27.068][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-09 16:04:27.069][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-08-09 16:04:27.075][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-09 16:04:27.077][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2025-08-09 16:04:27.081][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-08-09 16:04:27.083][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2025-08-09 16:04:27.085][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-09 16:04:27.087][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-09 16:04:27.089][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-08-09 16:04:27.091][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-08-09 16:04:27.093][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-08-09 16:04:27.095][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-09 16:04:27.097][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-08-09 16:04:27.099][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-09 16:04:27.101][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-08-09 16:04:27.103][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2025-08-09 16:04:27.105][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-09 16:04:27.107][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-08-09 16:04:27.109][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-08-09 16:04:27.111][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>". biodb.DEBUG[2025-08-09 16:04:27.113][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-08-09 16:04:27.115][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:04:27.117][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:04:27.119][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-09 16:04:27.120][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:04:27.121][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:04:27.122][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-09 16:04:27.124][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-08-09 16:04:27.125][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-09 16:04:27.126][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-09 16:04:27.127][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-08-09 16:04:27.128][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-09 16:04:27.130][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-08-09 16:04:27.131][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.132][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[2025-08-09 16:04:27.133][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:27.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:27.139][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:27.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.143][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[2025-08-09 16:04:27.144][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:27.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:27.150][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:27.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:27.155][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:27.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:27.161][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:27.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:27.166][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:27.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:27.172][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:27.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:27.177][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:27.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:27.183][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:27.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:27.188][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:27.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:27.194][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:27.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:27.199][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:27.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:27.205][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:27.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:27.210][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:27.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:27.216][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:27.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:27.221][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2025-08-09 16:04:27.223][self$getEntryFields()$define] Define field description. biodb.DEBUG[2025-08-09 16:04:27.224][self$getEntryFields()$define] Define field name. biodb.DEBUG[2025-08-09 16:04:27.226][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2025-08-09 16:04:27.228][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2025-08-09 16:04:27.229][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2025-08-09 16:04:27.231][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2025-08-09 16:04:27.232][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2025-08-09 16:04:27.239][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2025-08-09 16:04:27.240][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2025-08-09 16:04:27.242][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2025-08-09 16:04:27.244][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2025-08-09 16:04:27.245][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2025-08-09 16:04:27.247][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2025-08-09 16:04:27.248][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2025-08-09 16:04:27.250][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2025-08-09 16:04:27.251][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2025-08-09 16:04:27.253][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2025-08-09 16:04:27.255][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2025-08-09 16:04:27.256][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2025-08-09 16:04:27.258][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2025-08-09 16:04:27.259][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2025-08-09 16:04:27.261][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2025-08-09 16:04:27.263][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2025-08-09 16:04:27.264][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2025-08-09 16:04:27.266][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2025-08-09 16:04:27.267][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2025-08-09 16:04:27.269][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2025-08-09 16:04:27.271][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2025-08-09 16:04:27.272][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2025-08-09 16:04:27.274][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2025-08-09 16:04:27.275][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2025-08-09 16:04:27.277][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2025-08-09 16:04:27.278][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2025-08-09 16:04:27.280][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2025-08-09 16:04:27.282][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2025-08-09 16:04:27.283][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2025-08-09 16:04:27.285][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2025-08-09 16:04:27.286][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2025-08-09 16:04:27.288][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2025-08-09 16:04:27.289][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2025-08-09 16:04:27.291][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2025-08-09 16:04:27.293][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2025-08-09 16:04:27.294][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2025-08-09 16:04:27.296][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2025-08-09 16:04:27.297][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2025-08-09 16:04:27.299][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2025-08-09 16:04:27.300][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2025-08-09 16:04:27.302][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2025-08-09 16:04:27.304][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2025-08-09 16:04:27.305][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2025-08-09 16:04:27.307][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2025-08-09 16:04:27.308][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2025-08-09 16:04:27.310][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2025-08-09 16:04:27.312][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2025-08-09 16:04:27.313][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2025-08-09 16:04:27.315][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2025-08-09 16:04:27.316][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2025-08-09 16:04:27.318][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2025-08-09 16:04:27.319][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2025-08-09 16:04:27.321][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2025-08-09 16:04:27.323][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2025-08-09 16:04:27.324][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2025-08-09 16:04:27.326][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2025-08-09 16:04:27.327][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2025-08-09 16:04:27.329][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2025-08-09 16:04:27.331][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2025-08-09 16:04:27.332][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2025-08-09 16:04:27.334][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2025-08-09 16:04:27.335][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2025-08-09 16:04:27.337][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2025-08-09 16:04:27.338][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2025-08-09 16:04:27.340][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2025-08-09 16:04:27.342][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2025-08-09 16:04:27.343][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2025-08-09 16:04:27.345][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2025-08-09 16:04:27.346][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2025-08-09 16:04:27.348][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2025-08-09 16:04:27.349][self$getEntryFields()$define] Define field products. biodb.DEBUG[2025-08-09 16:04:27.351][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2025-08-09 16:04:27.353][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2025-08-09 16:04:27.354][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2025-08-09 16:04:27.356][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2025-08-09 16:04:27.357][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2025-08-09 16:04:27.360][initialize] This is biodb version 1.17.1. biodb.DEBUG[2025-08-09 16:04:27.361][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-08-09 16:04:27.362][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.364][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:27.367][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:27.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:27.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:27.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:27.380][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:27.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:27.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:27.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:27.388][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:27.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:27.390][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:27.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.394][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[2025-08-09 16:04:27.395][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:27.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:27.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:27.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.402][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[2025-08-09 16:04:27.403][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:27.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:27.405][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:27.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.410][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:27.411][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:27.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:27.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:27.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:27.418][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:27.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:27.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:27.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:27.426][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:27.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:27.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:27.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.432][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[2025-08-09 16:04:27.434][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:27.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:27.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:27.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:27.441][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:27.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:27.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:27.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:27.449][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:27.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:27.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:27.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:27.457][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:27.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:27.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:27.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.461][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:27.464][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:27.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:27.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:27.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:27.472][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:27.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:27.474][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:27.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:27.480][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:27.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:27.482][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:27.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:27.487][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:04:27.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:27.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:27.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:04:27.497][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml". biodb.DEBUG[2025-08-09 16:04:27.499][self$getDbsInfo()$define] Define connector nci.cactus. biodb.DEBUG[2025-08-09 16:04:27.501][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-08-09 16:04:27.502][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.". biodb.DEBUG[2025-08-09 16:04:27.503][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-09 16:04:27.505][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-09 16:04:27.506][self$setPropertyValue] Setting property "downloadable" to "TRUE". biodb.DEBUG[2025-08-09 16:04:27.507][self$setPropertyValue] Setting property "dwnld.ext" to "gz". biodb.DEBUG[2025-08-09 16:04:27.508][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2025-08-09 16:04:27.510][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-09 16:04:27.511][self$setPropertyValue] Setting property "entry.content.type" to "sdf". biodb.DEBUG[2025-08-09 16:04:27.512][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-09 16:04:27.513][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-08-09 16:04:27.514][self$setPropertyValue] Setting property "name" to "NCI CACTUS". biodb.DEBUG[2025-08-09 16:04:27.516][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-09 16:04:27.517][self$setPropertyValue] Setting property "parsing.expr" to "NSC". biodb.DEBUG[2025-08-09 16:04:27.517][self$setPropertyValue] Setting property "parsing.expr" to "DTP names". biodb.DEBUG[2025-08-09 16:04:27.517][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI". biodb.DEBUG[2025-08-09 16:04:27.517][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")". biodb.DEBUG[2025-08-09 16:04:27.517][self$setPropertyValue] Setting property "parsing.expr" to "Formula". biodb.DEBUG[2025-08-09 16:04:27.517][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight". biodb.DEBUG[2025-08-09 16:04:27.517][self$setPropertyValue] Setting property "parsing.expr" to "CAS". biodb.DEBUG[2025-08-09 16:04:27.523][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2025-08-09 16:04:27.524][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>". biodb.DEBUG[2025-08-09 16:04:27.526][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2025-08-09 16:04:27.527][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:04:27.528][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:04:27.529][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-09 16:04:27.530][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:04:27.531][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:04:27.532][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-09 16:04:27.534][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/". biodb.DEBUG[2025-08-09 16:04:27.534][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/". biodb.DEBUG[2025-08-09 16:04:27.534][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/". biodb.DEBUG[2025-08-09 16:04:27.534][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz". biodb.DEBUG[2025-08-09 16:04:27.535][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-09 16:04:27.536][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-09 16:04:27.537][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2025-08-09 16:04:27.538][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-09 16:04:27.540][self$getEntryFields()$define] Define field nci.cactus.id. biodb.DEBUG[2025-08-09 16:04:27.543][super$initialize] Initialize connector nci.cactus. biodb.DEBUG[2025-08-09 16:04:27.561][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus . biodb.INFO [2025-08-09 16:04:27.562][biodb$terminate] Closing BiodbMain instance... biodb.INFO [2025-08-09 16:04:27.563][self$deleteConn] Connector "nci.cactus" deleted. biodb.DEBUG[2025-08-09 16:04:27.565][notifyObservers] Notify observers for terminate. biodb.DEBUG[2025-08-09 16:04:27.566][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:04:27.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:04:27.568][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:04:27.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:04:27.570][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:04:27.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". [ FAIL 2 | WARN 0 | SKIP 0 | PASS 85 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_long_100_generic.R:37:1'): RT unit is defined when there is an RT value. ── Error in `private$doExtractDownload()`: attempt to apply non-function Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, opt = `<named list>`) 3. └─conn$getBiodb()$getFactory()$getEntry(...) 4. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE) 5. └─conn$getEntryContent(ids) 6. └─self$download() 7. └─private$doExtractDownload() ── Error ('test_long_100_generic.R:37:1'): We can load an entry from the database. ── Error in `cch$getTmpFolderPath()`: attempt to apply non-function Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, opt = `<named list>`) 3. └─opt$refEntries$getRealEntry(id) 4. └─self$getRealEntries(ids = id) 5. └─private$bdb$getFactory()$getEntry(...) 6. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE) 7. └─conn$getEntryContent(ids) 8. └─self$download() 9. └─private$doExtractDownload() [ FAIL 2 | WARN 0 | SKIP 0 | PASS 85 ] Error: Test failures Execution halted
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.22-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_1.13.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck' * using R version 4.5.1 (2025-06-13 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * 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 '1.13.1' * 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) 14.2.0' * 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 whether startup messages can be suppressed ... 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' ERROR Running the tests in 'longtests/testthat.R' failed. Last 13 lines of output: Backtrace: ▆ 1. ├─base::do.call(fct, params) 2. └─biodb (local) `<fn>`(conn = `<NcCctsCn>`, opt = `<named list>`) 3. └─opt$refEntries$getRealEntry(id) 4. └─self$getRealEntries(ids = id) 5. └─private$bdb$getFactory()$getEntry(...) 6. └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE) 7. └─conn$getEntryContent(ids) 8. └─self$download() 9. └─private$doExtractDownload() [ FAIL 2 | WARN 0 | SKIP 0 | PASS 85 ] Error: Test failures Execution halted * DONE Status: 1 ERROR, 1 NOTE See 'F:/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/00check.log' for details.
biodbNci.Rcheck/00install.out
* installing *source* package 'biodbNci' ... ** this is package 'biodbNci' version '1.13.1' ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 14.2.0' g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/testthat/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/testthat/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c extractEntries.cpp -o extractEntries.o g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/testthat/include' -I"C:/rtools45/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"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.22-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.22-bioc/R/library/testthat/include' -I"C:/rtools45/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:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.22-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 Warning in fun(libname, pkgname) : Package 'biodbNci' is deprecated and will be removed from Bioconductor version 3.23 ** testing if installed package can be loaded from final location Warning in fun(libname, pkgname) : Package 'biodbNci' is deprecated and will be removed from Bioconductor version 3.23 ** testing if installed package keeps a record of temporary installation path * DONE (biodbNci)