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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.13.1.tar.gz |
StartedAt: 2025-08-09 16:01:22 -0400 (Sat, 09 Aug 2025) |
EndedAt: 2025-08-09 16:02:16 -0400 (Sat, 09 Aug 2025) |
EllapsedTime: 54.7 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: biodbNci.Rcheck |
Warnings: NA |
biodbNci.Rcheck/tests/testthat.Rout.fail
R version 4.5.1 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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 16:02:13.063][biodb::testContext] biodb.INFO [2025-08-09 16:02:13.067][biodb::testContext] ******************************************************************************** biodb.INFO [2025-08-09 16:02:13.068][biodb::testContext] Test context - Generic long tests biodb.INFO [2025-08-09 16:02:13.069][biodb::testContext] ******************************************************************************** biodb.INFO [2025-08-09 16:02:13.070][biodb::testContext] biodb.INFO [2025-08-09 16:02:13.076][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1. biodb.DEBUG[2025-08-09 16:02:13.078][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml". biodb.DEBUG[2025-08-09 16:02:13.085][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-08-09 16:02:13.086][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2025-08-09 16:02:13.088][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2025-08-09 16:02:13.089][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:13.093][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2025-08-09 16:02:13.108][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2025-08-09 16:02:13.109][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:13.111][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2025-08-09 16:02:13.112][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2025-08-09 16:02:13.113][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:13.116][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2025-08-09 16:02:13.117][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2025-08-09 16:02:13.118][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2025-08-09 16:02:13.119][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:13.121][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2025-08-09 16:02:13.122][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2025-08-09 16:02:13.123][self$set] Set key cache.system to TRUE. biodb.DEBUG[2025-08-09 16:02:13.124][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:13.126][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2025-08-09 16:02:13.127][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2025-08-09 16:02:13.128][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:13.130][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2025-08-09 16:02:13.131][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2025-08-09 16:02:13.132][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2025-08-09 16:02:13.133][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:13.135][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2025-08-09 16:02:13.136][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2025-08-09 16:02:13.137][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.138][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 16:02:13.139][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2025-08-09 16:02:13.140][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2025-08-09 16:02:13.141][self$set] Set key force.locale to TRUE. biodb.DEBUG[2025-08-09 16:02:13.141][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:13.144][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2025-08-09 16:02:13.145][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2025-08-09 16:02:13.146][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2025-08-09 16:02:13.146][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2025-08-09 16:02:13.147][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2025-08-09 16:02:13.148][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2025-08-09 16:02:13.149][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:13.151][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2025-08-09 16:02:13.152][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2025-08-09 16:02:13.152][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:13.155][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2025-08-09 16:02:13.155][self$set] Set key entries.sep to "|". biodb.DEBUG[2025-08-09 16:02:13.156][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:13.159][self$getConfig()$define] Define config key offline. biodb.DEBUG[2025-08-09 16:02:13.160][self$set] Set key offline to FALSE. biodb.DEBUG[2025-08-09 16:02:13.160][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:13.163][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2025-08-09 16:02:13.164][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2025-08-09 16:02:13.165][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2025-08-09 16:02:13.166][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:13.169][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2025-08-09 16:02:13.170][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2025-08-09 16:02:13.187][self$set] Set key svn.binary.path to "". biodb.DEBUG[2025-08-09 16:02:13.188][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:13.190][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2025-08-09 16:02:13.191][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2025-08-09 16:02:13.192][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2025-08-09 16:02:13.193][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:13.201][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2025-08-09 16:02:13.225][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-08-09 16:02:13.238][self$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 16:02:13.239][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-09 16:02:13.240][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-09 16:02:13.240][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-08-09 16:02:13.241][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-08-09 16:02:13.242][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-08-09 16:02:13.243][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-09 16:02:13.244][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-08-09 16:02:13.245][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-09 16:02:13.245][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-08-09 16:02:13.246][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2025-08-09 16:02:13.247][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-09 16:02:13.248][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-08-09 16:02:13.249][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-08-09 16:02:13.249][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-08-09 16:02:13.249][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-08-09 16:02:13.249][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-08-09 16:02:13.249][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-08-09 16:02:13.249][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-08-09 16:02:13.250][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-08-09 16:02:13.251][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:02:13.252][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:02:13.253][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-09 16:02:13.253][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:02:13.254][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:02:13.255][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-09 16:02:13.255][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-08-09 16:02:13.256][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-09 16:02:13.257][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-09 16:02:13.258][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-08-09 16:02:13.259][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-09 16:02:13.260][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2025-08-09 16:02:13.261][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-08-09 16:02:13.262][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2025-08-09 16:02:13.263][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-09 16:02:13.263][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-09 16:02:13.264][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-08-09 16:02:13.265][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-08-09 16:02:13.266][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-08-09 16:02:13.267][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-09 16:02:13.267][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-08-09 16:02:13.268][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-09 16:02:13.269][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-08-09 16:02:13.270][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2025-08-09 16:02:13.271][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-09 16:02:13.272][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-08-09 16:02:13.272][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-08-09 16:02:13.273][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-08-09 16:02:13.273][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-08-09 16:02:13.273][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-08-09 16:02:13.273][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-08-09 16:02:13.273][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-08-09 16:02:13.274][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-08-09 16:02:13.275][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:02:13.276][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:02:13.276][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-09 16:02:13.277][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:02:13.278][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:02:13.279][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-09 16:02:13.279][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-08-09 16:02:13.280][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-09 16:02:13.281][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-09 16:02:13.281][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-08-09 16:02:13.282][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-09 16:02:13.283][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2025-08-09 16:02:13.284][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-08-09 16:02:13.285][self$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 16:02:13.286][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-09 16:02:13.287][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-09 16:02:13.288][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-08-09 16:02:13.289][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-08-09 16:02:13.289][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-08-09 16:02:13.290][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-09 16:02:13.291][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-08-09 16:02:13.292][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-09 16:02:13.292][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-08-09 16:02:13.293][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2025-08-09 16:02:13.294][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-09 16:02:13.295][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-08-09 16:02:13.296][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-08-09 16:02:13.297][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>". biodb.DEBUG[2025-08-09 16:02:13.297][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-08-09 16:02:13.298][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:02:13.299][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:02:13.300][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-09 16:02:13.300][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:02:13.301][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:02:13.302][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-09 16:02:13.303][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-08-09 16:02:13.304][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-09 16:02:13.304][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-09 16:02:13.305][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-08-09 16:02:13.306][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-09 16:02:13.307][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2025-08-09 16:02:13.308][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-08-09 16:02:13.309][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2025-08-09 16:02:13.310][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-09 16:02:13.311][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-09 16:02:13.311][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-08-09 16:02:13.312][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-08-09 16:02:13.313][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-08-09 16:02:13.314][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-09 16:02:13.314][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-08-09 16:02:13.315][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-09 16:02:13.316][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-08-09 16:02:13.317][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2025-08-09 16:02:13.318][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-09 16:02:13.319][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-08-09 16:02:13.320][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-08-09 16:02:13.320][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>". biodb.DEBUG[2025-08-09 16:02:13.321][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-08-09 16:02:13.322][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:02:13.323][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:02:13.324][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-09 16:02:13.324][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:02:13.325][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:02:13.326][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-09 16:02:13.327][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-08-09 16:02:13.328][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-09 16:02:13.328][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-09 16:02:13.329][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-08-09 16:02:13.330][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-09 16:02:13.333][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-08-09 16:02:13.334][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:13.335][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:02:13.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:13.343][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.344][FUN] 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 16:02:13.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:13.346][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:02:13.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:13.350][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:02:13.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:13.354][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.355][FUN] 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 16:02:13.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:13.357][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.359][FUN] 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 16:02:13.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:13.361][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:02:13.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:13.364][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:02:13.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:13.368][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.369][FUN] 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 16:02:13.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:13.372][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:02:13.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:13.375][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.376][FUN] 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 16:02:13.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:13.379][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.380][FUN] 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 16:02:13.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:13.382][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.384][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 16:02:13.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:13.386][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.387][FUN] 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 16:02:13.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:13.389][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:02:13.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:13.393][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:02:13.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.396][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 16:02:13.396][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2025-08-09 16:02:13.400][self$getEntryFields()$define] Define field description. biodb.DEBUG[2025-08-09 16:02:13.401][self$getEntryFields()$define] Define field name. biodb.DEBUG[2025-08-09 16:02:13.402][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2025-08-09 16:02:13.404][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2025-08-09 16:02:13.405][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2025-08-09 16:02:13.406][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2025-08-09 16:02:13.407][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2025-08-09 16:02:13.408][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2025-08-09 16:02:13.409][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2025-08-09 16:02:13.411][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2025-08-09 16:02:13.412][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2025-08-09 16:02:13.413][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2025-08-09 16:02:13.414][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2025-08-09 16:02:13.415][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2025-08-09 16:02:13.416][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2025-08-09 16:02:13.418][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2025-08-09 16:02:13.419][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2025-08-09 16:02:13.420][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2025-08-09 16:02:13.421][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2025-08-09 16:02:13.422][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2025-08-09 16:02:13.423][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2025-08-09 16:02:13.425][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2025-08-09 16:02:13.426][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2025-08-09 16:02:13.427][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2025-08-09 16:02:13.428][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2025-08-09 16:02:13.429][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2025-08-09 16:02:13.430][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2025-08-09 16:02:13.431][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2025-08-09 16:02:13.433][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2025-08-09 16:02:13.434][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2025-08-09 16:02:13.435][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2025-08-09 16:02:13.436][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2025-08-09 16:02:13.437][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2025-08-09 16:02:13.438][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2025-08-09 16:02:13.440][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2025-08-09 16:02:13.441][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2025-08-09 16:02:13.442][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2025-08-09 16:02:13.443][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2025-08-09 16:02:13.444][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2025-08-09 16:02:13.445][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2025-08-09 16:02:13.446][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2025-08-09 16:02:13.448][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2025-08-09 16:02:13.449][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2025-08-09 16:02:13.450][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2025-08-09 16:02:13.451][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2025-08-09 16:02:13.452][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2025-08-09 16:02:13.453][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2025-08-09 16:02:13.454][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2025-08-09 16:02:13.455][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2025-08-09 16:02:13.457][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2025-08-09 16:02:13.458][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2025-08-09 16:02:13.459][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2025-08-09 16:02:13.460][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2025-08-09 16:02:13.461][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2025-08-09 16:02:13.462][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2025-08-09 16:02:13.464][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2025-08-09 16:02:13.465][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2025-08-09 16:02:13.466][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2025-08-09 16:02:13.467][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2025-08-09 16:02:13.468][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2025-08-09 16:02:13.469][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2025-08-09 16:02:13.470][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2025-08-09 16:02:13.471][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2025-08-09 16:02:13.472][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2025-08-09 16:02:13.474][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2025-08-09 16:02:13.475][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2025-08-09 16:02:13.476][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2025-08-09 16:02:13.477][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2025-08-09 16:02:13.478][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2025-08-09 16:02:13.479][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2025-08-09 16:02:13.485][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2025-08-09 16:02:13.486][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2025-08-09 16:02:13.487][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2025-08-09 16:02:13.488][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2025-08-09 16:02:13.489][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2025-08-09 16:02:13.490][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2025-08-09 16:02:13.492][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2025-08-09 16:02:13.493][self$getEntryFields()$define] Define field products. biodb.DEBUG[2025-08-09 16:02:13.494][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2025-08-09 16:02:13.495][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2025-08-09 16:02:13.496][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2025-08-09 16:02:13.497][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2025-08-09 16:02:13.502][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2025-08-09 16:02:13.504][initialize] This is biodb version 1.17.1. biodb.DEBUG[2025-08-09 16:02:13.506][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-08-09 16:02:13.507][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.508][FUN] 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 16:02:13.509][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:13.513][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:13.515][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:13.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:02:13.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:13.518][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:13.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:13.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.521][FUN] 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 16:02:13.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:13.524][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:13.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:13.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.526][FUN] 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 16:02:13.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:13.529][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:13.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:13.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:02:13.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:13.534][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:13.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:13.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.537][FUN] 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 16:02:13.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:13.539][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:13.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:13.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:02:13.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:13.544][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:13.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:13.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.547][FUN] 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 16:02:13.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:13.549][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:13.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:13.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.552][FUN] 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 16:02:13.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:13.554][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:13.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:13.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.557][FUN] 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 16:02:13.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:13.559][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:13.561][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:13.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:02:13.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:13.565][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:13.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:13.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.568][FUN] 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 16:02:13.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:13.570][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:13.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:13.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.573][FUN] 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 16:02:13.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:13.575][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:13.577][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:13.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:02:13.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:13.581][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:13.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:13.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:02:13.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:13.587][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:13.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:13.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.590][FUN] 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 16:02:13.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:13.593][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:13.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:13.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:13.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:02:13.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:13.599][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml". biodb.DEBUG[2025-08-09 16:02:13.608][self$getDbsInfo()$define] Define connector nci.cactus. biodb.DEBUG[2025-08-09 16:02:13.610][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-08-09 16:02:13.611][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.". biodb.DEBUG[2025-08-09 16:02:13.612][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-09 16:02:13.612][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-09 16:02:13.613][self$setPropertyValue] Setting property "downloadable" to "TRUE". biodb.DEBUG[2025-08-09 16:02:13.614][self$setPropertyValue] Setting property "dwnld.ext" to "gz". biodb.DEBUG[2025-08-09 16:02:13.615][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2025-08-09 16:02:13.616][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-09 16:02:13.617][self$setPropertyValue] Setting property "entry.content.type" to "sdf". biodb.DEBUG[2025-08-09 16:02:13.618][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-09 16:02:13.618][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-08-09 16:02:13.619][self$setPropertyValue] Setting property "name" to "NCI CACTUS". biodb.DEBUG[2025-08-09 16:02:13.620][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-09 16:02:13.621][self$setPropertyValue] Setting property "parsing.expr" to "NSC". biodb.DEBUG[2025-08-09 16:02:13.621][self$setPropertyValue] Setting property "parsing.expr" to "DTP names". biodb.DEBUG[2025-08-09 16:02:13.621][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI". biodb.DEBUG[2025-08-09 16:02:13.621][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")". biodb.DEBUG[2025-08-09 16:02:13.621][self$setPropertyValue] Setting property "parsing.expr" to "Formula". biodb.DEBUG[2025-08-09 16:02:13.621][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight". biodb.DEBUG[2025-08-09 16:02:13.621][self$setPropertyValue] Setting property "parsing.expr" to "CAS". biodb.DEBUG[2025-08-09 16:02:13.622][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2025-08-09 16:02:13.623][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>". biodb.DEBUG[2025-08-09 16:02:13.624][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2025-08-09 16:02:13.625][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:02:13.625][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:02:13.626][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-09 16:02:13.627][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:02:13.628][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:02:13.632][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-09 16:02:13.633][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/". biodb.DEBUG[2025-08-09 16:02:13.633][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/". biodb.DEBUG[2025-08-09 16:02:13.633][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/". biodb.DEBUG[2025-08-09 16:02:13.633][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz". biodb.DEBUG[2025-08-09 16:02:13.634][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-09 16:02:13.635][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-09 16:02:13.636][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2025-08-09 16:02:13.636][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-09 16:02:13.641][self$getEntryFields()$define] Define field nci.cactus.id. biodb.DEBUG[2025-08-09 16:02:13.660][super$initialize] Initialize connector nci.cactus. biodb.DEBUG[2025-08-09 16:02:13.675][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus . biodb.INFO [2025-08-09 16:02:13.682][biodb::testThat] biodb.INFO [2025-08-09 16:02:13.683][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value "). biodb.INFO [2025-08-09 16:02:13.684][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-09 16:02:13.685][biodb::testThat] biodb.TRACE[2025-08-09 16:02:13.688][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf". biodb.DEBUG[2025-08-09 16:02:13.689][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s). biodb.DEBUG[2025-08-09 16:02:13.692][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries. biodb.DEBUG[2025-08-09 16:02:13.698][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-08-09 16:02:13.699][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:13.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:13.713][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:13.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:02:13.715][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:13.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-08-09 16:02:13.732][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:13.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:13.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.736][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:13.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:13.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.749][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.751][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:02:13.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:02:13.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.754][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.776][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:02:13.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:02:13.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.779][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.781][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:02:13.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:02:13.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.783][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.784][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:02:13.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:02:13.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.787][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.788][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:02:13.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:02:13.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.791][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.792][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:02:13.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:02:13.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.795][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.797][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:02:13.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:02:13.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.800][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.801][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:02:13.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:02:13.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.813][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.815][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:02:13.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:02:13.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.817][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.818][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:02:13.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:02:13.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:13.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:13.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.824][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.825][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:02:13.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:02:13.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.828][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:13.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:13.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.832][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:13.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:13.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.835][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:13.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:13.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.839][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:13.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:13.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.870][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:13.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:13.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.874][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:13.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:13.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.877][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-08-09 16:02:13.878][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674. biodb.TRACE[2025-08-09 16:02:13.880][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-08-09 16:02:13.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-08-09 16:02:13.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.883][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.885][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-08-09 16:02:13.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-08-09 16:02:13.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.887][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.888][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2025-08-09 16:02:13.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2025-08-09 16:02:13.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.891][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.892][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2025-08-09 16:02:13.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2025-08-09 16:02:13.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.894][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:13.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:13.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.899][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.912][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:02:13.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:02:13.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.915][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:13.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:13.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.923][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:13.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:13.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.926][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.931][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:13.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:13.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.933][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:13.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:13.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.938][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:13.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:13.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.941][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:13.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:13.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.945][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:02:13.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:02:13.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.948][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:02:13.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:02:13.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.950][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.951][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:02:13.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:02:13.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.953][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:13.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:13.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.963][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:13.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:13.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.966][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:13.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:13.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.969][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.970][ef$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:13.971][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:13.972][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.973][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:13.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:13.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.976][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.984][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:02:13.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:02:13.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.987][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.988][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:02:13.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:02:13.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.990][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.991][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:02:13.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:02:13.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.993][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.994][ef$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:02:13.995][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:02:13.996][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:13.997][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:13.997][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:02:13.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:02:13.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.000][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.008][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:02:14.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:02:14.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.010][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.011][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:02:14.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:02:14.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.013][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.014][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:02:14.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:02:14.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.016][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.017][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:02:14.018][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:02:14.019][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.020][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.021][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:02:14.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:02:14.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.033][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:02:14.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:02:14.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.036][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.037][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:02:14.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:02:14.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.041][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.042][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:02:14.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:02:14.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.044][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.045][ef$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:02:14.046][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:02:14.047][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.048][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.048][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:02:14.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:02:14.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.051][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.064][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:02:14.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:02:14.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.067][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.068][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:02:14.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:02:14.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.071][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:02:14.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:02:14.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.074][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.075][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:02:14.076][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:02:14.076][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.077][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.078][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:02:14.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:02:14.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.081][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.089][ef$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:14.090][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:14.091][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.091][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.096][ef$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:02:14.097][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:02:14.098][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.099][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.103][ef$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:02:14.104][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:02:14.105][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.106][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.110][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:02:14.111][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:02:14.112][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.113][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.118][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:02:14.119][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:02:14.119][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.120][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.134][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf". biodb.DEBUG[2025-08-09 16:02:14.162][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s). biodb.DEBUG[2025-08-09 16:02:14.163][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries. biodb.DEBUG[2025-08-09 16:02:14.164][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-08-09 16:02:14.165][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:14.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:14.203][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:14.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:02:14.204][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:14.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-08-09 16:02:14.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:14.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:14.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.215][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:14.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:14.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.218][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.231][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-08-09 16:02:14.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-08-09 16:02:14.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.234][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.235][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-08-09 16:02:14.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-08-09 16:02:14.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.237][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.238][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:02:14.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:02:14.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.242][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:02:14.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:02:14.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.244][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.245][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:02:14.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:02:14.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.247][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.248][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:02:14.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:02:14.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.250][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.251][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:02:14.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:02:14.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.254][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.255][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:02:14.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:02:14.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.258][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:02:14.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:02:14.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.260][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.261][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:02:14.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:02:14.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.263][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.264][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:02:14.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:02:14.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.267][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.267][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:02:14.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:02:14.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.269][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.270][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:02:14.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:02:14.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.273][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.274][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:02:14.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:02:14.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.277][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.278][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:02:14.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:02:14.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.280][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.282][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:02:14.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:02:14.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.284][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.285][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:02:14.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:02:14.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.288][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.289][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:02:14.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:02:14.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.292][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.293][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:02:14.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:02:14.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.295][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:14.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:14.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.298][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.299][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:02:14.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:02:14.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.302][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:14.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:14.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.305][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.306][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:14.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:14.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.308][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.309][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:14.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:14.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.315][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:14.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:14.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.318][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:14.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:14.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.321][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:14.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:14.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.324][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-08-09 16:02:14.325][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690. biodb.TRACE[2025-08-09 16:02:14.340][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-08-09 16:02:14.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-08-09 16:02:14.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.343][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.344][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-08-09 16:02:14.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-08-09 16:02:14.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.346][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.347][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2025-08-09 16:02:14.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2025-08-09 16:02:14.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.349][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.350][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2025-08-09 16:02:14.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2025-08-09 16:02:14.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.352][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:14.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:14.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.356][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.360][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:02:14.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:02:14.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.363][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:14.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:14.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.369][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:14.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:14.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.372][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:14.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:14.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.375][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:14.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:14.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.380][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:14.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:14.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.383][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:14.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:14.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.386][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.387][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:02:14.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:02:14.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.389][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.390][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:02:14.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:02:14.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.392][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.393][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-09 16:02:14.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-09 16:02:14.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.396][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:14.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:14.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.413][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.414][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:14.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:14.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.416][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:14.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:14.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.423][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.424][ef$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:14.425][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:14.426][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.426][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:14.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:14.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.430][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.437][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-08-09 16:02:14.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-08-09 16:02:14.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.439][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.440][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-08-09 16:02:14.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-08-09 16:02:14.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.442][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.443][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-08-09 16:02:14.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-08-09 16:02:14.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.446][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.446][ef$get] Asked field names are: cas.id. biodb.TRACE[2025-08-09 16:02:14.447][ef$get] Realnames of fields are: cas.id. biodb.TRACE[2025-08-09 16:02:14.448][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.449][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.450][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-08-09 16:02:14.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-08-09 16:02:14.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.452][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.460][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:02:14.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:02:14.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.463][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.464][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:02:14.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:02:14.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.466][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.467][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:02:14.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:02:14.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.470][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.470][ef$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:02:14.471][ef$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:02:14.472][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.473][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.474][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:02:14.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:02:14.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.476][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.485][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:02:14.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:02:14.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.487][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.488][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:02:14.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:02:14.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.490][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.491][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:02:14.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:02:14.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.493][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.494][ef$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:02:14.495][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:02:14.496][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.497][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.498][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:02:14.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:02:14.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.500][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.508][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:02:14.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:02:14.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.510][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.511][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:02:14.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:02:14.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.514][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.514][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:02:14.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:02:14.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.517][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.518][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:02:14.519][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:02:14.519][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.520][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.521][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:02:14.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:02:14.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.524][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.532][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:02:14.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:02:14.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.535][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.536][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:02:14.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:02:14.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.538][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.539][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:02:14.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:02:14.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.542][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.547][ef$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:02:14.548][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:02:14.549][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.549][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.550][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:02:14.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:02:14.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.553][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.561][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:02:14.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:02:14.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.564][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.564][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:02:14.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:02:14.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.567][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.568][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:02:14.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:02:14.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.570][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.571][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:02:14.572][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:02:14.573][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.574][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.574][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:02:14.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:02:14.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.577][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.585][ef$get] Asked field names are: accession. biodb.TRACE[2025-08-09 16:02:14.586][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-08-09 16:02:14.587][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.588][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.593][ef$get] Asked field names are: cas.id. biodb.TRACE[2025-08-09 16:02:14.593][ef$get] Realnames of fields are: cas.id. biodb.TRACE[2025-08-09 16:02:14.594][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.595][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.599][ef$get] Asked field names are: formula. biodb.TRACE[2025-08-09 16:02:14.600][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-08-09 16:02:14.601][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.602][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.606][ef$get] Asked field names are: inchi. biodb.TRACE[2025-08-09 16:02:14.607][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-09 16:02:14.608][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.609][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.614][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-08-09 16:02:14.615][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-09 16:02:14.615][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.616][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.621][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-09 16:02:14.622][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-09 16:02:14.623][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.624][ef$get] fields variable is a list. biodb.TRACE[2025-08-09 16:02:14.629][ef$get] Asked field names are: name. biodb.TRACE[2025-08-09 16:02:14.630][ef$get] Realnames of fields are: name. biodb.TRACE[2025-08-09 16:02:14.631][ef$get] 1 fields were returned. biodb.TRACE[2025-08-09 16:02:14.631][ef$get] fields variable is a list. biodb.INFO [2025-08-09 16:02:14.642][biodb::testThat] biodb.INFO [2025-08-09 16:02:14.643][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. "). biodb.INFO [2025-08-09 16:02:14.644][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-09 16:02:14.644][biodb::testThat] biodb.DEBUG[2025-08-09 16:02:14.647][private$loadEntries] Creating entries from ids [2]: "749674, 750690". biodb.DEBUG[2025-08-09 16:02:14.652][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)... biodb.DEBUG[2025-08-09 16:02:14.654][self$isDownloaded] Database nci.cactus has already been downloaded. biodb.DEBUG[2025-08-09 16:02:14.683][self$isDownloaded] Database nci.cactus has already been downloaded. biodb.INFO [2025-08-09 16:02:14.685][self$download] Extract whole database of nci.cactus. biodb.INFO [2025-08-09 16:02:14.686][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database.... biodb.INFO [2025-08-09 16:02:14.728][biodb::testThat] biodb.INFO [2025-08-09 16:02:14.730][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field "). biodb.INFO [2025-08-09 16:02:14.731][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-09 16:02:14.732][biodb::testThat] biodb.INFO [2025-08-09 16:02:14.740][biodb::testThat] biodb.INFO [2025-08-09 16:02:14.741][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. "). biodb.INFO [2025-08-09 16:02:14.742][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-09 16:02:14.743][biodb::testThat] biodb.WARN [2025-08-09 16:02:14.764][self$searchForEntries] This database is not searchable by field "name". biodb.WARN [2025-08-09 16:02:14.783][self$searchForEntries] This database is not searchable by field "name". biodb.INFO [2025-08-09 16:02:14.793][biodb::testThat] biodb.INFO [2025-08-09 16:02:14.794][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. "). biodb.INFO [2025-08-09 16:02:14.795][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-09 16:02:14.796][biodb::testThat] biodb.DEBUG[2025-08-09 16:02:14.816][private$loadEntries] Creating entries from ids [1]: "749674". biodb.DEBUG[2025-08-09 16:02:14.862][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)... biodb.DEBUG[2025-08-09 16:02:14.864][self$isDownloaded] Database nci.cactus has already been downloaded. biodb.DEBUG[2025-08-09 16:02:14.865][self$isDownloaded] Database nci.cactus has already been downloaded. biodb.INFO [2025-08-09 16:02:14.866][self$download] Extract whole database of nci.cactus. biodb.INFO [2025-08-09 16:02:14.876][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database.... biodb.INFO [2025-08-09 16:02:14.897][biodb::testThat] biodb.INFO [2025-08-09 16:02:14.898][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. "). biodb.INFO [2025-08-09 16:02:14.899][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-09 16:02:14.899][biodb::testThat] biodb.INFO [2025-08-09 16:02:14.906][biodb::testThat] biodb.INFO [2025-08-09 16:02:14.907][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. "). biodb.INFO [2025-08-09 16:02:14.908][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-09 16:02:14.909][biodb::testThat] biodb.INFO [2025-08-09 16:02:14.915][biodb::testThat] biodb.INFO [2025-08-09 16:02:14.916][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. "). biodb.INFO [2025-08-09 16:02:14.916][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-09 16:02:14.917][biodb::testThat] biodb.INFO [2025-08-09 16:02:14.927][biodb::testThat] biodb.INFO [2025-08-09 16:02:14.928][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. "). biodb.INFO [2025-08-09 16:02:14.929][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-09 16:02:14.929][biodb::testThat] biodb.INFO [2025-08-09 16:02:14.935][biodb$terminate] Closing BiodbMain instance... biodb.INFO [2025-08-09 16:02:14.936][self$deleteConn] Connector "nci.cactus" deleted. biodb.DEBUG[2025-08-09 16:02:14.937][notifyObservers] Notify observers for terminate. biodb.DEBUG[2025-08-09 16:02:14.937][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:14.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:14.939][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:14.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:02:14.940][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:14.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.INFO [2025-08-09 16:02:14.949][biodb::testContext] biodb.INFO [2025-08-09 16:02:14.950][biodb::testContext] ******************************************************************************** biodb.INFO [2025-08-09 16:02:14.951][biodb::testContext] Test context - Example long tests biodb.INFO [2025-08-09 16:02:14.951][biodb::testContext] ******************************************************************************** biodb.INFO [2025-08-09 16:02:14.952][biodb::testContext] biodb.INFO [2025-08-09 16:02:14.954][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1. biodb.DEBUG[2025-08-09 16:02:14.955][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/biodb/definitions.yml". biodb.DEBUG[2025-08-09 16:02:14.958][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-08-09 16:02:14.959][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2025-08-09 16:02:14.960][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2025-08-09 16:02:14.961][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:14.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:14.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:14.963][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2025-08-09 16:02:14.964][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2025-08-09 16:02:14.965][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:14.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:14.966][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:14.967][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2025-08-09 16:02:14.968][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2025-08-09 16:02:14.968][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:14.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:14.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:14.971][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2025-08-09 16:02:14.971][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2025-08-09 16:02:14.972][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2025-08-09 16:02:14.973][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:14.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:14.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:14.975][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2025-08-09 16:02:14.976][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2025-08-09 16:02:14.977][self$set] Set key cache.system to TRUE. biodb.DEBUG[2025-08-09 16:02:14.978][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:14.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:14.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:14.980][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2025-08-09 16:02:14.981][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2025-08-09 16:02:14.981][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:14.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:14.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:14.984][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2025-08-09 16:02:14.984][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2025-08-09 16:02:14.985][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2025-08-09 16:02:14.986][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:14.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:14.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:14.988][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2025-08-09 16:02:14.989][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2025-08-09 16:02:14.990][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:14.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:14.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:14.992][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2025-08-09 16:02:14.993][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2025-08-09 16:02:14.994][self$set] Set key force.locale to TRUE. biodb.DEBUG[2025-08-09 16:02:14.994][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:14.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:14.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:14.997][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2025-08-09 16:02:14.997][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2025-08-09 16:02:14.998][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2025-08-09 16:02:14.999][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2025-08-09 16:02:15.000][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2025-08-09 16:02:15.001][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2025-08-09 16:02:15.001][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:15.004][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2025-08-09 16:02:15.004][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2025-08-09 16:02:15.005][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.007][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 16:02:15.007][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2025-08-09 16:02:15.008][self$set] Set key entries.sep to "|". biodb.DEBUG[2025-08-09 16:02:15.009][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:15.011][self$getConfig()$define] Define config key offline. biodb.DEBUG[2025-08-09 16:02:15.012][self$set] Set key offline to FALSE. biodb.DEBUG[2025-08-09 16:02:15.013][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.014][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 16:02:15.015][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2025-08-09 16:02:15.016][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2025-08-09 16:02:15.017][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2025-08-09 16:02:15.018][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:15.020][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2025-08-09 16:02:15.021][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2025-08-09 16:02:15.041][self$set] Set key svn.binary.path to "". biodb.DEBUG[2025-08-09 16:02:15.042][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:15.044][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2025-08-09 16:02:15.045][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2025-08-09 16:02:15.046][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2025-08-09 16:02:15.047][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:15.049][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2025-08-09 16:02:15.050][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-08-09 16:02:15.051][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2025-08-09 16:02:15.052][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-09 16:02:15.057][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-09 16:02:15.057][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-08-09 16:02:15.058][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-08-09 16:02:15.059][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-08-09 16:02:15.060][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-09 16:02:15.060][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-08-09 16:02:15.061][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-09 16:02:15.062][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-08-09 16:02:15.063][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2025-08-09 16:02:15.063][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-09 16:02:15.064][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-08-09 16:02:15.065][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-08-09 16:02:15.066][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-08-09 16:02:15.066][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-08-09 16:02:15.066][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-08-09 16:02:15.066][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-08-09 16:02:15.066][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-08-09 16:02:15.067][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-08-09 16:02:15.067][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:02:15.068][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:02:15.069][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-09 16:02:15.070][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:02:15.070][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:02:15.071][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-09 16:02:15.072][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-08-09 16:02:15.073][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-09 16:02:15.074][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-09 16:02:15.074][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-08-09 16:02:15.075][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-09 16:02:15.076][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2025-08-09 16:02:15.077][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-08-09 16:02:15.078][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2025-08-09 16:02:15.079][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-09 16:02:15.080][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-09 16:02:15.081][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-08-09 16:02:15.081][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-08-09 16:02:15.082][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-08-09 16:02:15.083][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-09 16:02:15.084][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-08-09 16:02:15.084][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-09 16:02:15.085][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-08-09 16:02:15.086][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2025-08-09 16:02:15.087][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-09 16:02:15.087][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-08-09 16:02:15.088][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-08-09 16:02:15.089][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-08-09 16:02:15.089][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-08-09 16:02:15.089][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-08-09 16:02:15.089][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-08-09 16:02:15.089][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-08-09 16:02:15.090][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-08-09 16:02:15.090][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:02:15.091][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:02:15.092][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-09 16:02:15.093][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:02:15.093][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:02:15.094][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-09 16:02:15.095][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-08-09 16:02:15.096][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-09 16:02:15.096][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-09 16:02:15.097][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-08-09 16:02:15.098][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-09 16:02:15.099][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2025-08-09 16:02:15.100][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-08-09 16:02:15.101][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2025-08-09 16:02:15.102][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-09 16:02:15.103][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-09 16:02:15.103][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-08-09 16:02:15.104][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-08-09 16:02:15.105][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-08-09 16:02:15.105][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-09 16:02:15.106][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-08-09 16:02:15.107][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-09 16:02:15.108][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-08-09 16:02:15.108][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2025-08-09 16:02:15.109][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-09 16:02:15.110][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-08-09 16:02:15.111][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-08-09 16:02:15.111][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>". biodb.DEBUG[2025-08-09 16:02:15.112][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-08-09 16:02:15.113][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:02:15.114][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:02:15.114][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-09 16:02:15.115][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:02:15.116][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:02:15.117][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-09 16:02:15.118][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-08-09 16:02:15.118][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-09 16:02:15.119][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-09 16:02:15.120][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-08-09 16:02:15.121][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-09 16:02:15.122][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2025-08-09 16:02:15.123][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-08-09 16:02:15.124][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2025-08-09 16:02:15.125][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-09 16:02:15.125][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-09 16:02:15.126][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-08-09 16:02:15.127][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-08-09 16:02:15.128][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-08-09 16:02:15.129][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-09 16:02:15.130][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-08-09 16:02:15.130][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-09 16:02:15.131][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-08-09 16:02:15.132][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2025-08-09 16:02:15.133][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-09 16:02:15.134][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-08-09 16:02:15.134][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-08-09 16:02:15.135][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>". biodb.DEBUG[2025-08-09 16:02:15.136][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-08-09 16:02:15.137][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:02:15.138][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:02:15.138][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-09 16:02:15.139][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:02:15.140][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:02:15.141][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-09 16:02:15.142][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-08-09 16:02:15.143][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-09 16:02:15.143][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-09 16:02:15.144][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-08-09 16:02:15.145][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-09 16:02:15.146][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-08-09 16:02:15.147][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:15.148][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.149][FUN] 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 16:02:15.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:15.152][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:02:15.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:15.155][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.157][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 16:02:15.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:15.163][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.165][FUN] 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 16:02:15.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:15.167][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.168][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 16:02:15.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:15.170][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:02:15.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:15.174][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.175][FUN] 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 16:02:15.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:15.177][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.179][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 16:02:15.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:15.181][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:02:15.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:15.184][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:02:15.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.187][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 16:02:15.188][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.189][FUN] 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 16:02:15.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:15.191][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.193][FUN] 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 16:02:15.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:15.195][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.196][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 16:02:15.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.198][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 16:02:15.198][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.199][FUN] 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 16:02:15.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:15.201][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.203][FUN] 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 16:02:15.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.204][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 16:02:15.205][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:02:15.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:15.208][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2025-08-09 16:02:15.209][self$getEntryFields()$define] Define field description. biodb.DEBUG[2025-08-09 16:02:15.210][self$getEntryFields()$define] Define field name. biodb.DEBUG[2025-08-09 16:02:15.211][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2025-08-09 16:02:15.212][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2025-08-09 16:02:15.214][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2025-08-09 16:02:15.215][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2025-08-09 16:02:15.216][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2025-08-09 16:02:15.217][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2025-08-09 16:02:15.218][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2025-08-09 16:02:15.219][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2025-08-09 16:02:15.220][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2025-08-09 16:02:15.221][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2025-08-09 16:02:15.222][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2025-08-09 16:02:15.223][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2025-08-09 16:02:15.224][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2025-08-09 16:02:15.225][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2025-08-09 16:02:15.226][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2025-08-09 16:02:15.227][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2025-08-09 16:02:15.228][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2025-08-09 16:02:15.229][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2025-08-09 16:02:15.231][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2025-08-09 16:02:15.232][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2025-08-09 16:02:15.233][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2025-08-09 16:02:15.234][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2025-08-09 16:02:15.235][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2025-08-09 16:02:15.236][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2025-08-09 16:02:15.237][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2025-08-09 16:02:15.238][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2025-08-09 16:02:15.240][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2025-08-09 16:02:15.241][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2025-08-09 16:02:15.242][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2025-08-09 16:02:15.243][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2025-08-09 16:02:15.244][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2025-08-09 16:02:15.245][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2025-08-09 16:02:15.247][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2025-08-09 16:02:15.248][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2025-08-09 16:02:15.249][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2025-08-09 16:02:15.250][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2025-08-09 16:02:15.251][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2025-08-09 16:02:15.252][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2025-08-09 16:02:15.254][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2025-08-09 16:02:15.255][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2025-08-09 16:02:15.256][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2025-08-09 16:02:15.257][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2025-08-09 16:02:15.258][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2025-08-09 16:02:15.259][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2025-08-09 16:02:15.264][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2025-08-09 16:02:15.266][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2025-08-09 16:02:15.267][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2025-08-09 16:02:15.268][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2025-08-09 16:02:15.269][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2025-08-09 16:02:15.270][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2025-08-09 16:02:15.271][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2025-08-09 16:02:15.272][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2025-08-09 16:02:15.273][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2025-08-09 16:02:15.274][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2025-08-09 16:02:15.275][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2025-08-09 16:02:15.276][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2025-08-09 16:02:15.278][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2025-08-09 16:02:15.279][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2025-08-09 16:02:15.280][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2025-08-09 16:02:15.281][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2025-08-09 16:02:15.282][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2025-08-09 16:02:15.283][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2025-08-09 16:02:15.284][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2025-08-09 16:02:15.285][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2025-08-09 16:02:15.287][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2025-08-09 16:02:15.288][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2025-08-09 16:02:15.289][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2025-08-09 16:02:15.290][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2025-08-09 16:02:15.291][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2025-08-09 16:02:15.292][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2025-08-09 16:02:15.294][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2025-08-09 16:02:15.295][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2025-08-09 16:02:15.296][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2025-08-09 16:02:15.297][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2025-08-09 16:02:15.298][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2025-08-09 16:02:15.299][self$getEntryFields()$define] Define field products. biodb.DEBUG[2025-08-09 16:02:15.300][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2025-08-09 16:02:15.301][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2025-08-09 16:02:15.303][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2025-08-09 16:02:15.304][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2025-08-09 16:02:15.305][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2025-08-09 16:02:15.306][initialize] This is biodb version 1.17.1. biodb.DEBUG[2025-08-09 16:02:15.307][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-08-09 16:02:15.308][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:02:15.309][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:15.311][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:15.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:15.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:02:15.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:15.316][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:15.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:15.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.319][FUN] 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 16:02:15.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:15.321][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:15.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:15.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.324][FUN] 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 16:02:15.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:15.326][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:15.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:15.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:02:15.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:15.332][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:15.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:15.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.334][FUN] 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 16:02:15.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:15.337][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:15.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:15.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:02:15.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:15.342][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:15.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:15.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.345][FUN] 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 16:02:15.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:15.348][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:15.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:15.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.351][FUN] 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 16:02:15.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:15.353][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:15.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:15.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:02:15.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:15.359][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:15.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:15.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.363][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 16:02:15.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:15.365][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:15.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:15.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.368][FUN] 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 16:02:15.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:15.376][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:15.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:15.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:02:15.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-09 16:02:15.382][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:15.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:15.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:02:15.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:15.388][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:15.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:15.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-09 16:02:15.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:15.393][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:15.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:15.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.397][FUN] 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 16:02:15.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:15.399][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-09 16:02:15.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:15.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:15.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.402][FUN] 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 16:02:15.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_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 16:02:15.406][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml". biodb.DEBUG[2025-08-09 16:02:15.407][self$getDbsInfo()$define] Define connector nci.cactus. biodb.DEBUG[2025-08-09 16:02:15.409][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-08-09 16:02:15.409][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.". biodb.DEBUG[2025-08-09 16:02:15.410][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-09 16:02:15.411][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-09 16:02:15.412][self$setPropertyValue] Setting property "downloadable" to "TRUE". biodb.DEBUG[2025-08-09 16:02:15.413][self$setPropertyValue] Setting property "dwnld.ext" to "gz". biodb.DEBUG[2025-08-09 16:02:15.414][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2025-08-09 16:02:15.415][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-09 16:02:15.415][self$setPropertyValue] Setting property "entry.content.type" to "sdf". biodb.DEBUG[2025-08-09 16:02:15.416][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-09 16:02:15.417][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-08-09 16:02:15.418][self$setPropertyValue] Setting property "name" to "NCI CACTUS". biodb.DEBUG[2025-08-09 16:02:15.419][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-09 16:02:15.420][self$setPropertyValue] Setting property "parsing.expr" to "NSC". biodb.DEBUG[2025-08-09 16:02:15.420][self$setPropertyValue] Setting property "parsing.expr" to "DTP names". biodb.DEBUG[2025-08-09 16:02:15.420][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI". biodb.DEBUG[2025-08-09 16:02:15.420][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")". biodb.DEBUG[2025-08-09 16:02:15.420][self$setPropertyValue] Setting property "parsing.expr" to "Formula". biodb.DEBUG[2025-08-09 16:02:15.420][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight". biodb.DEBUG[2025-08-09 16:02:15.420][self$setPropertyValue] Setting property "parsing.expr" to "CAS". biodb.DEBUG[2025-08-09 16:02:15.420][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2025-08-09 16:02:15.421][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>". biodb.DEBUG[2025-08-09 16:02:15.422][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2025-08-09 16:02:15.423][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:02:15.424][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:02:15.425][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-09 16:02:15.425][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-09 16:02:15.426][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-09 16:02:15.427][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-09 16:02:15.428][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/". biodb.DEBUG[2025-08-09 16:02:15.428][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/". biodb.DEBUG[2025-08-09 16:02:15.428][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/". biodb.DEBUG[2025-08-09 16:02:15.428][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz". biodb.DEBUG[2025-08-09 16:02:15.429][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-09 16:02:15.430][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-09 16:02:15.431][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2025-08-09 16:02:15.432][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-09 16:02:15.433][self$getEntryFields()$define] Define field nci.cactus.id. biodb.DEBUG[2025-08-09 16:02:15.435][super$initialize] Initialize connector nci.cactus. biodb.DEBUG[2025-08-09 16:02:15.441][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus . biodb.INFO [2025-08-09 16:02:15.441][biodb$terminate] Closing BiodbMain instance... biodb.INFO [2025-08-09 16:02:15.442][self$deleteConn] Connector "nci.cactus" deleted. biodb.DEBUG[2025-08-09 16:02:15.443][notifyObservers] Notify observers for terminate. biodb.DEBUG[2025-08-09 16:02:15.444][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-09 16:02:15.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-09 16:02:15.445][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2025-08-09 16:02:15.446][FUN] 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 16:02:15.447][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2025-08-09 16:02:15.448][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". [ 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: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.13.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’ * checking for file ‘biodbNci/DESCRIPTION’ ... OK * this is package ‘biodbNci’ version ‘1.13.1’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘biodbNci’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking 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 ‘/Users/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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c extractEntries.cpp -o extractEntries.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c test-100-example.cpp -o test-100-example.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c test-runner.cpp -o test-runner.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R installing to /Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning in fun(libname, pkgname) : Package 'biodbNci' is deprecated and will be removed from Bioconductor version 3.23 ** checking absolute paths in shared objects and dynamic libraries ** 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)