Back to Long Tests report for BioC 3.22 |
This page was generated on 2025-08-02 23:55 -0400 (Sat, 02 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" | 4796 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4535 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4578 |
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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.13.1.tar.gz |
StartedAt: 2025-08-02 16:02:33 -0400 (Sat, 02 Aug 2025) |
EndedAt: 2025-08-02 16:03:31 -0400 (Sat, 02 Aug 2025) |
EllapsedTime: 58.0 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-pc-linux-gnu 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 [2025-08-02 16:03:28.267][biodb::testContext] biodb.INFO [2025-08-02 16:03:28.268][biodb::testContext] ******************************************************************************** biodb.INFO [2025-08-02 16:03:28.269][biodb::testContext] Test context - Generic long tests biodb.INFO [2025-08-02 16:03:28.270][biodb::testContext] ******************************************************************************** biodb.INFO [2025-08-02 16:03:28.271][biodb::testContext] biodb.INFO [2025-08-02 16:03:28.277][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1. biodb.DEBUG[2025-08-02 16:03:28.279][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml". biodb.DEBUG[2025-08-02 16:03:28.285][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-08-02 16:03:28.286][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2025-08-02 16:03:28.287][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2025-08-02 16:03:28.288][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.291][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2025-08-02 16:03:28.308][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2025-08-02 16:03:28.308][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.310][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[2025-08-02 16:03:28.311][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2025-08-02 16:03:28.312][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2025-08-02 16:03:28.313][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.315][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2025-08-02 16:03:28.316][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2025-08-02 16:03:28.317][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2025-08-02 16:03:28.318][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.320][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[2025-08-02 16:03:28.321][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2025-08-02 16:03:28.322][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2025-08-02 16:03:28.323][self$set] Set key cache.system to TRUE. biodb.DEBUG[2025-08-02 16:03:28.323][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.326][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2025-08-02 16:03:28.327][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2025-08-02 16:03:28.328][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.330][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2025-08-02 16:03:28.331][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2025-08-02 16:03:28.332][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2025-08-02 16:03:28.333][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.335][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2025-08-02 16:03:28.336][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2025-08-02 16:03:28.337][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.340][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2025-08-02 16:03:28.341][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2025-08-02 16:03:28.342][self$set] Set key force.locale to TRUE. biodb.DEBUG[2025-08-02 16:03:28.342][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.345][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2025-08-02 16:03:28.346][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2025-08-02 16:03:28.347][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2025-08-02 16:03:28.348][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2025-08-02 16:03:28.349][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2025-08-02 16:03:28.350][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2025-08-02 16:03:28.351][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.352][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[2025-08-02 16:03:28.353][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2025-08-02 16:03:28.354][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2025-08-02 16:03:28.355][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.357][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2025-08-02 16:03:28.358][self$set] Set key entries.sep to "|". biodb.DEBUG[2025-08-02 16:03:28.359][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.362][self$getConfig()$define] Define config key offline. biodb.DEBUG[2025-08-02 16:03:28.363][self$set] Set key offline to FALSE. biodb.DEBUG[2025-08-02 16:03:28.364][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.366][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2025-08-02 16:03:28.367][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2025-08-02 16:03:28.368][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2025-08-02 16:03:28.369][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.371][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2025-08-02 16:03:28.372][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2025-08-02 16:03:28.376][self$set] Set key svn.binary.path to "". biodb.DEBUG[2025-08-02 16:03:28.377][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.380][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2025-08-02 16:03:28.381][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2025-08-02 16:03:28.381][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2025-08-02 16:03:28.387][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.389][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[2025-08-02 16:03:28.392][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2025-08-02 16:03:28.424][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-08-02 16:03:28.438][self$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[2025-08-02 16:03:28.439][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-02 16:03:28.440][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-02 16:03:28.441][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-08-02 16:03:28.442][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-08-02 16:03:28.443][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-08-02 16:03:28.444][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-02 16:03:28.445][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-08-02 16:03:28.446][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-02 16:03:28.447][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-08-02 16:03:28.448][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2025-08-02 16:03:28.449][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-02 16:03:28.450][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-08-02 16:03:28.451][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-08-02 16:03:28.452][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-08-02 16:03:28.452][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-08-02 16:03:28.452][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-08-02 16:03:28.452][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-08-02 16:03:28.452][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-08-02 16:03:28.452][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-08-02 16:03:28.453][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-02 16:03:28.454][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-02 16:03:28.455][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-02 16:03:28.456][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-02 16:03:28.457][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-02 16:03:28.458][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-02 16:03:28.459][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-08-02 16:03:28.460][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-02 16:03:28.460][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-02 16:03:28.461][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-08-02 16:03:28.462][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-02 16:03:28.463][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2025-08-02 16:03:28.465][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-08-02 16:03:28.466][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2025-08-02 16:03:28.467][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-02 16:03:28.468][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-02 16:03:28.469][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-08-02 16:03:28.470][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-08-02 16:03:28.471][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-08-02 16:03:28.472][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-02 16:03:28.472][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-08-02 16:03:28.473][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-02 16:03:28.474][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-08-02 16:03:28.475][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2025-08-02 16:03:28.476][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-02 16:03:28.477][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-08-02 16:03:28.478][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-08-02 16:03:28.479][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-08-02 16:03:28.479][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-08-02 16:03:28.479][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-08-02 16:03:28.479][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-08-02 16:03:28.479][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-08-02 16:03:28.480][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-08-02 16:03:28.481][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-02 16:03:28.482][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-02 16:03:28.483][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-02 16:03:28.483][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-02 16:03:28.484][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-02 16:03:28.485][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-02 16:03:28.486][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-08-02 16:03:28.487][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-02 16:03:28.488][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-02 16:03:28.489][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-08-02 16:03:28.490][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-02 16:03:28.491][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2025-08-02 16:03:28.492][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-08-02 16:03:28.493][self$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[2025-08-02 16:03:28.494][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-02 16:03:28.495][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-02 16:03:28.496][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-08-02 16:03:28.497][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-08-02 16:03:28.498][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-08-02 16:03:28.499][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-02 16:03:28.500][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-08-02 16:03:28.501][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-02 16:03:28.502][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-08-02 16:03:28.502][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2025-08-02 16:03:28.503][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-02 16:03:28.504][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-08-02 16:03:28.505][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-08-02 16:03:28.506][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>". biodb.DEBUG[2025-08-02 16:03:28.507][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-08-02 16:03:28.508][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-02 16:03:28.509][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-02 16:03:28.510][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-02 16:03:28.511][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-02 16:03:28.511][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-02 16:03:28.512][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-02 16:03:28.513][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-08-02 16:03:28.514][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-02 16:03:28.515][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-02 16:03:28.516][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-08-02 16:03:28.517][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-02 16:03:28.518][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2025-08-02 16:03:28.519][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-08-02 16:03:28.520][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2025-08-02 16:03:28.521][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-02 16:03:28.522][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-02 16:03:28.523][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-08-02 16:03:28.524][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-08-02 16:03:28.525][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-08-02 16:03:28.526][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-02 16:03:28.527][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-08-02 16:03:28.528][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-02 16:03:28.529][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-08-02 16:03:28.529][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2025-08-02 16:03:28.530][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-02 16:03:28.531][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-08-02 16:03:28.532][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-08-02 16:03:28.533][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>". biodb.DEBUG[2025-08-02 16:03:28.534][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-08-02 16:03:28.535][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-02 16:03:28.536][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-02 16:03:28.537][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-02 16:03:28.538][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-02 16:03:28.538][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-02 16:03:28.539][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-02 16:03:28.540][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-08-02 16:03:28.541][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-02 16:03:28.542][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-02 16:03:28.543][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-08-02 16:03:28.544][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-02 16:03:28.547][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-08-02 16:03:28.553][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.554][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:28.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:28.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.559][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:28.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:28.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.563][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:28.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:28.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.567][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:28.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:28.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.571][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:28.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:28.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.574][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[2025-08-02 16:03:28.575][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:28.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:28.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.579][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:28.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:28.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.583][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:28.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:28.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.586][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[2025-08-02 16:03:28.587][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:28.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:28.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.591][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:28.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:28.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.595][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:28.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:28.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.600][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:28.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:28.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.604][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:28.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:28.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.608][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:28.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:28.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.612][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:28.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:28.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.616][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:28.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:28.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.620][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2025-08-02 16:03:28.624][self$getEntryFields()$define] Define field description. biodb.DEBUG[2025-08-02 16:03:28.626][self$getEntryFields()$define] Define field name. biodb.DEBUG[2025-08-02 16:03:28.627][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2025-08-02 16:03:28.628][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2025-08-02 16:03:28.630][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2025-08-02 16:03:28.631][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2025-08-02 16:03:28.632][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2025-08-02 16:03:28.633][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2025-08-02 16:03:28.635][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2025-08-02 16:03:28.636][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2025-08-02 16:03:28.637][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2025-08-02 16:03:28.638][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2025-08-02 16:03:28.640][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2025-08-02 16:03:28.641][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2025-08-02 16:03:28.642][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2025-08-02 16:03:28.644][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2025-08-02 16:03:28.645][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2025-08-02 16:03:28.646][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2025-08-02 16:03:28.647][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2025-08-02 16:03:28.649][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2025-08-02 16:03:28.650][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2025-08-02 16:03:28.651][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2025-08-02 16:03:28.653][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2025-08-02 16:03:28.654][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2025-08-02 16:03:28.655][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2025-08-02 16:03:28.656][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2025-08-02 16:03:28.658][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2025-08-02 16:03:28.659][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2025-08-02 16:03:28.660][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2025-08-02 16:03:28.662][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2025-08-02 16:03:28.663][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2025-08-02 16:03:28.664][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2025-08-02 16:03:28.665][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2025-08-02 16:03:28.667][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2025-08-02 16:03:28.668][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2025-08-02 16:03:28.669][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2025-08-02 16:03:28.671][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2025-08-02 16:03:28.672][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2025-08-02 16:03:28.673][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2025-08-02 16:03:28.674][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2025-08-02 16:03:28.676][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2025-08-02 16:03:28.677][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2025-08-02 16:03:28.678][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2025-08-02 16:03:28.680][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2025-08-02 16:03:28.681][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2025-08-02 16:03:28.682][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2025-08-02 16:03:28.683][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2025-08-02 16:03:28.685][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2025-08-02 16:03:28.686][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2025-08-02 16:03:28.687][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2025-08-02 16:03:28.689][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2025-08-02 16:03:28.690][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2025-08-02 16:03:28.691][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2025-08-02 16:03:28.692][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2025-08-02 16:03:28.694][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2025-08-02 16:03:28.695][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2025-08-02 16:03:28.696][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2025-08-02 16:03:28.698][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2025-08-02 16:03:28.699][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2025-08-02 16:03:28.700][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2025-08-02 16:03:28.701][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2025-08-02 16:03:28.703][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2025-08-02 16:03:28.704][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2025-08-02 16:03:28.705][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2025-08-02 16:03:28.706][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2025-08-02 16:03:28.708][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2025-08-02 16:03:28.709][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2025-08-02 16:03:28.715][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2025-08-02 16:03:28.716][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2025-08-02 16:03:28.717][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2025-08-02 16:03:28.718][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2025-08-02 16:03:28.720][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2025-08-02 16:03:28.721][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2025-08-02 16:03:28.722][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2025-08-02 16:03:28.723][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2025-08-02 16:03:28.725][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2025-08-02 16:03:28.726][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2025-08-02 16:03:28.727][self$getEntryFields()$define] Define field products. biodb.DEBUG[2025-08-02 16:03:28.729][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2025-08-02 16:03:28.730][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2025-08-02 16:03:28.731][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2025-08-02 16:03:28.733][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2025-08-02 16:03:28.738][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2025-08-02 16:03:28.740][initialize] This is biodb version 1.17.1. biodb.DEBUG[2025-08-02 16:03:28.743][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-08-02 16:03:28.743][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:28.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:28.745][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.750][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:28.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:28.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:28.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:28.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.756][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:28.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:28.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:28.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:28.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.762][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:28.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:28.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:28.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:28.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.767][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:28.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:28.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:28.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:28.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.773][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:28.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:28.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:28.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:28.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.779][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:28.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:28.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:28.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:28.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.785][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:28.786][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:28.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:28.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:28.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.790][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:28.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:28.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:28.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:28.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.796][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:28.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:28.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:28.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:28.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.802][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:28.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:28.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:28.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:28.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.807][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:28.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:28.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:28.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:28.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.813][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:28.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:28.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:28.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:28.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.828][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:28.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:28.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:28.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:28.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.835][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:28.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:28.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:28.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:28.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.841][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:28.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:28.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:28.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:28.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.848][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:28.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:28.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:28.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:28.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:28.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:28.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:28.857][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml". biodb.DEBUG[2025-08-02 16:03:28.868][self$getDbsInfo()$define] Define connector nci.cactus. biodb.DEBUG[2025-08-02 16:03:28.871][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-08-02 16:03:28.872][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.". biodb.DEBUG[2025-08-02 16:03:28.873][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-02 16:03:28.874][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-02 16:03:28.875][self$setPropertyValue] Setting property "downloadable" to "TRUE". biodb.DEBUG[2025-08-02 16:03:28.876][self$setPropertyValue] Setting property "dwnld.ext" to "gz". biodb.DEBUG[2025-08-02 16:03:28.877][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2025-08-02 16:03:28.878][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-02 16:03:28.879][self$setPropertyValue] Setting property "entry.content.type" to "sdf". biodb.DEBUG[2025-08-02 16:03:28.880][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-02 16:03:28.881][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-08-02 16:03:28.882][self$setPropertyValue] Setting property "name" to "NCI CACTUS". biodb.DEBUG[2025-08-02 16:03:28.883][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-02 16:03:28.884][self$setPropertyValue] Setting property "parsing.expr" to "NSC". biodb.DEBUG[2025-08-02 16:03:28.884][self$setPropertyValue] Setting property "parsing.expr" to "DTP names". biodb.DEBUG[2025-08-02 16:03:28.884][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI". biodb.DEBUG[2025-08-02 16:03:28.884][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")". biodb.DEBUG[2025-08-02 16:03:28.884][self$setPropertyValue] Setting property "parsing.expr" to "Formula". biodb.DEBUG[2025-08-02 16:03:28.884][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight". biodb.DEBUG[2025-08-02 16:03:28.884][self$setPropertyValue] Setting property "parsing.expr" to "CAS". biodb.DEBUG[2025-08-02 16:03:28.886][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2025-08-02 16:03:28.887][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>". biodb.DEBUG[2025-08-02 16:03:28.902][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2025-08-02 16:03:28.903][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-02 16:03:28.904][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-02 16:03:28.905][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-02 16:03:28.906][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-02 16:03:28.907][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-02 16:03:28.908][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-02 16:03:28.909][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/". biodb.DEBUG[2025-08-02 16:03:28.909][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/". biodb.DEBUG[2025-08-02 16:03:28.909][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/". biodb.DEBUG[2025-08-02 16:03:28.909][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz". biodb.DEBUG[2025-08-02 16:03:28.910][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-02 16:03:28.911][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-02 16:03:28.912][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2025-08-02 16:03:28.913][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-02 16:03:28.920][self$getEntryFields()$define] Define field nci.cactus.id. biodb.DEBUG[2025-08-02 16:03:28.942][super$initialize] Initialize connector nci.cactus. biodb.DEBUG[2025-08-02 16:03:28.958][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus . biodb.INFO [2025-08-02 16:03:28.967][biodb::testThat] biodb.INFO [2025-08-02 16:03:28.968][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value "). biodb.INFO [2025-08-02 16:03:28.969][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-02 16:03:28.970][biodb::testThat] biodb.TRACE[2025-08-02 16:03:28.973][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf". biodb.DEBUG[2025-08-02 16:03:28.975][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s). biodb.DEBUG[2025-08-02 16:03:28.978][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries. biodb.DEBUG[2025-08-02 16:03:28.986][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-08-02 16:03:28.987][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:28.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:29.000][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:29.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:29.002][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:29.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-08-02 16:03:29.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.024][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.040][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.042][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-02 16:03:29.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-02 16:03:29.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.045][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.069][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-02 16:03:29.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-02 16:03:29.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.072][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.074][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-02 16:03:29.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-02 16:03:29.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.076][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.077][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-02 16:03:29.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-02 16:03:29.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.080][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.082][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-02 16:03:29.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-02 16:03:29.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.085][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.086][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-02 16:03:29.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-02 16:03:29.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.097][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.098][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-02 16:03:29.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-02 16:03:29.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.101][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.102][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-02 16:03:29.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-02 16:03:29.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.104][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.106][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-02 16:03:29.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-02 16:03:29.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.109][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.110][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-02 16:03:29.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-02 16:03:29.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.112][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.116][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.117][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-02 16:03:29.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-02 16:03:29.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.120][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.123][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.127][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.131][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.165][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.168][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.172][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-08-02 16:03:29.173][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674. biodb.TRACE[2025-08-02 16:03:29.175][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-08-02 16:03:29.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-08-02 16:03:29.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.178][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.179][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-08-02 16:03:29.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-08-02 16:03:29.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.181][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.182][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2025-08-02 16:03:29.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2025-08-02 16:03:29.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.185][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.186][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2025-08-02 16:03:29.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2025-08-02 16:03:29.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.189][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.193][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.205][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-02 16:03:29.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-02 16:03:29.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.208][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.218][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.222][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.225][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.230][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.234][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.238][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.239][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-02 16:03:29.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-02 16:03:29.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.242][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.243][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-02 16:03:29.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-02 16:03:29.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.245][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.246][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-02 16:03:29.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-02 16:03:29.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.249][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.258][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.262][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.265][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.266][ef$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.267][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.268][ef$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.269][ef$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.273][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.280][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-02 16:03:29.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-02 16:03:29.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.283][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.284][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-02 16:03:29.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-02 16:03:29.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.287][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.288][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-02 16:03:29.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-02 16:03:29.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.290][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.291][ef$get] Asked field names are: formula. biodb.TRACE[2025-08-02 16:03:29.292][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-08-02 16:03:29.293][ef$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.294][ef$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.295][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-02 16:03:29.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-02 16:03:29.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.298][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.305][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-02 16:03:29.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-02 16:03:29.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.307][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.308][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-02 16:03:29.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-02 16:03:29.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.311][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.312][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-02 16:03:29.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-02 16:03:29.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.315][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.316][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-02 16:03:29.317][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-02 16:03:29.317][ef$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.318][ef$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.319][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-02 16:03:29.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-02 16:03:29.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.322][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.329][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-02 16:03:29.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-02 16:03:29.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.332][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.333][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-02 16:03:29.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-02 16:03:29.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.335][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.336][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-02 16:03:29.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-02 16:03:29.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.339][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.344][ef$get] Asked field names are: inchi. biodb.TRACE[2025-08-02 16:03:29.345][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-02 16:03:29.345][ef$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.346][ef$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.347][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-02 16:03:29.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-02 16:03:29.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.350][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.357][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-02 16:03:29.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-02 16:03:29.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.360][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.361][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-02 16:03:29.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-02 16:03:29.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.364][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.365][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-02 16:03:29.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-02 16:03:29.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.367][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.368][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-08-02 16:03:29.369][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-02 16:03:29.370][ef$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.371][ef$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.372][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-02 16:03:29.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-02 16:03:29.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.375][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.382][ef$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.383][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.384][ef$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.385][ef$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.388][ef$get] Asked field names are: formula. biodb.TRACE[2025-08-02 16:03:29.389][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-08-02 16:03:29.390][ef$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.391][ef$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.395][ef$get] Asked field names are: inchi. biodb.TRACE[2025-08-02 16:03:29.396][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-02 16:03:29.397][ef$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.398][ef$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.401][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-08-02 16:03:29.402][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-02 16:03:29.403][ef$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.404][ef$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.408][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-02 16:03:29.409][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-02 16:03:29.410][ef$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.411][ef$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.426][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf". biodb.DEBUG[2025-08-02 16:03:29.492][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s). biodb.DEBUG[2025-08-02 16:03:29.493][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries. biodb.DEBUG[2025-08-02 16:03:29.495][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2025-08-02 16:03:29.495][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:29.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:29.500][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:29.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:29.502][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:29.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2025-08-02 16:03:29.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.514][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.518][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.535][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-08-02 16:03:29.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-08-02 16:03:29.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.538][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.539][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-08-02 16:03:29.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-08-02 16:03:29.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.542][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.543][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-02 16:03:29.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-02 16:03:29.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.546][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.547][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-02 16:03:29.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-02 16:03:29.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.550][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.551][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-02 16:03:29.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-02 16:03:29.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.553][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.554][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-02 16:03:29.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-02 16:03:29.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.557][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.558][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-02 16:03:29.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-02 16:03:29.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.561][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.562][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-02 16:03:29.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-02 16:03:29.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.565][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.566][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-02 16:03:29.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-02 16:03:29.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.569][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.570][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-02 16:03:29.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-02 16:03:29.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.572][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.573][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-02 16:03:29.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-02 16:03:29.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.576][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.577][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-02 16:03:29.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-02 16:03:29.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.580][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.581][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-02 16:03:29.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-02 16:03:29.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.583][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.585][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-02 16:03:29.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-02 16:03:29.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.588][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.589][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-02 16:03:29.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-02 16:03:29.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.591][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.593][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-02 16:03:29.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-02 16:03:29.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.595][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.596][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-02 16:03:29.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-02 16:03:29.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.599][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.601][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-02 16:03:29.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-02 16:03:29.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.603][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.604][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-02 16:03:29.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-02 16:03:29.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.607][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.611][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.612][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-02 16:03:29.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-02 16:03:29.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.618][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.621][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.625][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.629][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.632][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.636][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.640][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2025-08-02 16:03:29.641][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690. biodb.TRACE[2025-08-02 16:03:29.660][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-08-02 16:03:29.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-08-02 16:03:29.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.663][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.664][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2025-08-02 16:03:29.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2025-08-02 16:03:29.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.666][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.667][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2025-08-02 16:03:29.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2025-08-02 16:03:29.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.670][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.671][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2025-08-02 16:03:29.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2025-08-02 16:03:29.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.674][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.678][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.682][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-02 16:03:29.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-02 16:03:29.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.685][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.692][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.696][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.699][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.704][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.708][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.712][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.713][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-02 16:03:29.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-02 16:03:29.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.716][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.716][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-02 16:03:29.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-02 16:03:29.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.719][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.720][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2025-08-02 16:03:29.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2025-08-02 16:03:29.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.723][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.745][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.749][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.752][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.753][ef$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.754][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.755][ef$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.756][ef$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.760][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.767][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-08-02 16:03:29.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-08-02 16:03:29.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.770][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.771][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-08-02 16:03:29.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-08-02 16:03:29.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.774][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.775][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-08-02 16:03:29.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-08-02 16:03:29.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.777][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.778][ef$get] Asked field names are: cas.id. biodb.TRACE[2025-08-02 16:03:29.779][ef$get] Realnames of fields are: cas.id. biodb.TRACE[2025-08-02 16:03:29.780][ef$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.781][ef$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.782][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2025-08-02 16:03:29.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2025-08-02 16:03:29.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.785][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.792][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-02 16:03:29.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-02 16:03:29.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.795][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.796][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-02 16:03:29.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-02 16:03:29.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.798][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.799][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-02 16:03:29.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-02 16:03:29.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.802][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.803][ef$get] Asked field names are: name. biodb.TRACE[2025-08-02 16:03:29.804][ef$get] Realnames of fields are: name. biodb.TRACE[2025-08-02 16:03:29.805][ef$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.806][ef$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.806][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2025-08-02 16:03:29.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2025-08-02 16:03:29.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.809][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.816][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-02 16:03:29.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-02 16:03:29.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.819][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.820][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-02 16:03:29.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-02 16:03:29.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.823][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.823][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-02 16:03:29.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-02 16:03:29.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.826][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.827][ef$get] Asked field names are: formula. biodb.TRACE[2025-08-02 16:03:29.828][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-08-02 16:03:29.829][ef$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.830][ef$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.831][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2025-08-02 16:03:29.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2025-08-02 16:03:29.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.833][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.841][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-02 16:03:29.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-02 16:03:29.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.843][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.844][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-02 16:03:29.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-02 16:03:29.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.847][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.848][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-02 16:03:29.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-02 16:03:29.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.851][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.852][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-02 16:03:29.853][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-02 16:03:29.854][ef$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.854][ef$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.855][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-02 16:03:29.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-02 16:03:29.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.858][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.869][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-02 16:03:29.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-02 16:03:29.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.872][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.873][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-02 16:03:29.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-02 16:03:29.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.876][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.877][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-02 16:03:29.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-02 16:03:29.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.879][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.880][ef$get] Asked field names are: inchi. biodb.TRACE[2025-08-02 16:03:29.881][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-02 16:03:29.882][ef$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.883][ef$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.884][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2025-08-02 16:03:29.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-02 16:03:29.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.887][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.894][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-02 16:03:29.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-02 16:03:29.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.897][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.898][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-02 16:03:29.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-02 16:03:29.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.900][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.901][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-02 16:03:29.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-02 16:03:29.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.904][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.905][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-08-02 16:03:29.906][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-02 16:03:29.907][ef$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.908][ef$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.909][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2025-08-02 16:03:29.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-02 16:03:29.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.911][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.919][ef$get] Asked field names are: accession. biodb.TRACE[2025-08-02 16:03:29.920][ef$get] Realnames of fields are: accession. biodb.TRACE[2025-08-02 16:03:29.920][ef$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.921][ef$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.925][ef$get] Asked field names are: cas.id. biodb.TRACE[2025-08-02 16:03:29.926][ef$get] Realnames of fields are: cas.id. biodb.TRACE[2025-08-02 16:03:29.927][ef$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.928][ef$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.932][ef$get] Asked field names are: formula. biodb.TRACE[2025-08-02 16:03:29.933][ef$get] Realnames of fields are: formula. biodb.TRACE[2025-08-02 16:03:29.933][ef$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.934][ef$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.938][ef$get] Asked field names are: inchi. biodb.TRACE[2025-08-02 16:03:29.939][ef$get] Realnames of fields are: inchi. biodb.TRACE[2025-08-02 16:03:29.940][ef$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.941][ef$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.944][ef$get] Asked field names are: inchikey. biodb.TRACE[2025-08-02 16:03:29.945][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2025-08-02 16:03:29.946][ef$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.947][ef$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.951][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2025-08-02 16:03:29.952][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2025-08-02 16:03:29.953][ef$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.954][ef$get] fields variable is a list. biodb.TRACE[2025-08-02 16:03:29.957][ef$get] Asked field names are: name. biodb.TRACE[2025-08-02 16:03:29.958][ef$get] Realnames of fields are: name. biodb.TRACE[2025-08-02 16:03:29.959][ef$get] 1 fields were returned. biodb.TRACE[2025-08-02 16:03:29.960][ef$get] fields variable is a list. biodb.INFO [2025-08-02 16:03:29.966][biodb::testThat] biodb.INFO [2025-08-02 16:03:29.967][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. "). biodb.INFO [2025-08-02 16:03:29.968][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-02 16:03:29.969][biodb::testThat] biodb.DEBUG[2025-08-02 16:03:29.971][private$loadEntries] Creating entries from ids [2]: "749674, 750690". biodb.DEBUG[2025-08-02 16:03:29.973][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)... biodb.DEBUG[2025-08-02 16:03:29.976][self$isDownloaded] Database nci.cactus has already been downloaded. biodb.DEBUG[2025-08-02 16:03:30.008][self$isDownloaded] Database nci.cactus has already been downloaded. biodb.INFO [2025-08-02 16:03:30.009][self$download] Extract whole database of nci.cactus. biodb.INFO [2025-08-02 16:03:30.010][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database.... biodb.INFO [2025-08-02 16:03:30.047][biodb::testThat] biodb.INFO [2025-08-02 16:03:30.048][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field "). biodb.INFO [2025-08-02 16:03:30.049][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-02 16:03:30.050][biodb::testThat] biodb.INFO [2025-08-02 16:03:30.055][biodb::testThat] biodb.INFO [2025-08-02 16:03:30.056][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. "). biodb.INFO [2025-08-02 16:03:30.057][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-02 16:03:30.058][biodb::testThat] biodb.WARN [2025-08-02 16:03:30.075][self$searchForEntries] This database is not searchable by field "name". biodb.WARN [2025-08-02 16:03:30.093][self$searchForEntries] This database is not searchable by field "name". biodb.INFO [2025-08-02 16:03:30.100][biodb::testThat] biodb.INFO [2025-08-02 16:03:30.101][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. "). biodb.INFO [2025-08-02 16:03:30.102][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-02 16:03:30.103][biodb::testThat] biodb.DEBUG[2025-08-02 16:03:30.124][private$loadEntries] Creating entries from ids [1]: "749674". biodb.DEBUG[2025-08-02 16:03:30.167][conn$getEntryContent] Get NCI CACTUS entry content(s) for 1 id(s)... biodb.DEBUG[2025-08-02 16:03:30.169][self$isDownloaded] Database nci.cactus has already been downloaded. biodb.DEBUG[2025-08-02 16:03:30.170][self$isDownloaded] Database nci.cactus has already been downloaded. biodb.INFO [2025-08-02 16:03:30.171][self$download] Extract whole database of nci.cactus. biodb.INFO [2025-08-02 16:03:30.183][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database.... biodb.INFO [2025-08-02 16:03:30.206][biodb::testThat] biodb.INFO [2025-08-02 16:03:30.207][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. "). biodb.INFO [2025-08-02 16:03:30.208][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-02 16:03:30.209][biodb::testThat] biodb.INFO [2025-08-02 16:03:30.219][biodb::testThat] biodb.INFO [2025-08-02 16:03:30.220][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. "). biodb.INFO [2025-08-02 16:03:30.221][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-02 16:03:30.221][biodb::testThat] biodb.INFO [2025-08-02 16:03:30.228][biodb::testThat] biodb.INFO [2025-08-02 16:03:30.228][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. "). biodb.INFO [2025-08-02 16:03:30.229][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-02 16:03:30.230][biodb::testThat] biodb.INFO [2025-08-02 16:03:30.235][biodb::testThat] biodb.INFO [2025-08-02 16:03:30.236][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. "). biodb.INFO [2025-08-02 16:03:30.237][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2025-08-02 16:03:30.238][biodb::testThat] biodb.INFO [2025-08-02 16:03:30.243][biodb$terminate] Closing BiodbMain instance... biodb.INFO [2025-08-02 16:03:30.244][self$deleteConn] Connector "nci.cactus" deleted. biodb.DEBUG[2025-08-02 16:03:30.245][notifyObservers] Notify observers for terminate. biodb.DEBUG[2025-08-02 16:03:30.246][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:30.247][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:30.248][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.249][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.INFO [2025-08-02 16:03:30.259][biodb::testContext] biodb.INFO [2025-08-02 16:03:30.260][biodb::testContext] ******************************************************************************** biodb.INFO [2025-08-02 16:03:30.260][biodb::testContext] Test context - Example long tests biodb.INFO [2025-08-02 16:03:30.261][biodb::testContext] ******************************************************************************** biodb.INFO [2025-08-02 16:03:30.262][biodb::testContext] biodb.INFO [2025-08-02 16:03:30.264][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.17.1. biodb.DEBUG[2025-08-02 16:03:30.266][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc/R/site-library/biodb/definitions.yml". biodb.DEBUG[2025-08-02 16:03:30.269][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-08-02 16:03:30.270][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2025-08-02 16:03:30.271][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2025-08-02 16:03:30.272][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.275][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2025-08-02 16:03:30.276][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2025-08-02 16:03:30.276][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.279][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2025-08-02 16:03:30.280][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2025-08-02 16:03:30.281][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.283][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2025-08-02 16:03:30.284][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2025-08-02 16:03:30.285][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2025-08-02 16:03:30.286][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.288][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2025-08-02 16:03:30.289][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2025-08-02 16:03:30.290][self$set] Set key cache.system to TRUE. biodb.DEBUG[2025-08-02 16:03:30.291][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.294][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2025-08-02 16:03:30.295][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2025-08-02 16:03:30.295][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.298][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2025-08-02 16:03:30.299][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2025-08-02 16:03:30.300][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2025-08-02 16:03:30.301][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.303][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2025-08-02 16:03:30.304][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2025-08-02 16:03:30.305][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.308][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2025-08-02 16:03:30.308][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2025-08-02 16:03:30.309][self$set] Set key force.locale to TRUE. biodb.DEBUG[2025-08-02 16:03:30.310][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.313][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2025-08-02 16:03:30.314][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2025-08-02 16:03:30.315][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2025-08-02 16:03:30.316][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2025-08-02 16:03:30.317][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2025-08-02 16:03:30.318][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2025-08-02 16:03:30.318][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.321][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2025-08-02 16:03:30.322][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2025-08-02 16:03:30.323][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.325][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2025-08-02 16:03:30.326][self$set] Set key entries.sep to "|". biodb.DEBUG[2025-08-02 16:03:30.327][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.330][self$getConfig()$define] Define config key offline. biodb.DEBUG[2025-08-02 16:03:30.331][self$set] Set key offline to FALSE. biodb.DEBUG[2025-08-02 16:03:30.331][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.334][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2025-08-02 16:03:30.335][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2025-08-02 16:03:30.336][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2025-08-02 16:03:30.337][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.343][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2025-08-02 16:03:30.344][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2025-08-02 16:03:30.348][self$set] Set key svn.binary.path to "". biodb.DEBUG[2025-08-02 16:03:30.349][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.352][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2025-08-02 16:03:30.352][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2025-08-02 16:03:30.353][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2025-08-02 16:03:30.354][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.357][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2025-08-02 16:03:30.359][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-08-02 16:03:30.360][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2025-08-02 16:03:30.361][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-02 16:03:30.361][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-02 16:03:30.362][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-08-02 16:03:30.363][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-08-02 16:03:30.364][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-08-02 16:03:30.365][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-02 16:03:30.366][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-08-02 16:03:30.367][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-02 16:03:30.368][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-08-02 16:03:30.369][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2025-08-02 16:03:30.370][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-02 16:03:30.371][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-08-02 16:03:30.372][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-08-02 16:03:30.373][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-08-02 16:03:30.373][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-08-02 16:03:30.373][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-08-02 16:03:30.373][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-08-02 16:03:30.373][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-08-02 16:03:30.374][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-08-02 16:03:30.375][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-02 16:03:30.376][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-02 16:03:30.376][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-02 16:03:30.377][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-02 16:03:30.378][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-02 16:03:30.379][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-02 16:03:30.380][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-08-02 16:03:30.381][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-02 16:03:30.382][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-02 16:03:30.383][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-08-02 16:03:30.384][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-02 16:03:30.385][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2025-08-02 16:03:30.386][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-08-02 16:03:30.387][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2025-08-02 16:03:30.388][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-02 16:03:30.389][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-02 16:03:30.390][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-08-02 16:03:30.391][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-08-02 16:03:30.392][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-08-02 16:03:30.393][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-02 16:03:30.394][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-08-02 16:03:30.395][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-02 16:03:30.396][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-08-02 16:03:30.397][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2025-08-02 16:03:30.398][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-02 16:03:30.399][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-08-02 16:03:30.400][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-08-02 16:03:30.400][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2025-08-02 16:03:30.400][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2025-08-02 16:03:30.400][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2025-08-02 16:03:30.400][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2025-08-02 16:03:30.400][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2025-08-02 16:03:30.401][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-08-02 16:03:30.402][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-02 16:03:30.403][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-02 16:03:30.404][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-02 16:03:30.405][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-02 16:03:30.406][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-02 16:03:30.407][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-02 16:03:30.408][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-08-02 16:03:30.408][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-02 16:03:30.409][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-02 16:03:30.410][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-08-02 16:03:30.411][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-02 16:03:30.412][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2025-08-02 16:03:30.414][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-08-02 16:03:30.415][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2025-08-02 16:03:30.416][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-02 16:03:30.417][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-02 16:03:30.418][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-08-02 16:03:30.418][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-08-02 16:03:30.419][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-08-02 16:03:30.420][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-02 16:03:30.421][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2025-08-02 16:03:30.422][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-02 16:03:30.423][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-08-02 16:03:30.424][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2025-08-02 16:03:30.425][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-02 16:03:30.426][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-08-02 16:03:30.427][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-08-02 16:03:30.428][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>". biodb.DEBUG[2025-08-02 16:03:30.429][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-08-02 16:03:30.429][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-02 16:03:30.430][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-02 16:03:30.431][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-02 16:03:30.432][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-02 16:03:30.433][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-02 16:03:30.434][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-02 16:03:30.435][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-08-02 16:03:30.436][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-02 16:03:30.436][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-02 16:03:30.437][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-08-02 16:03:30.438][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-02 16:03:30.439][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2025-08-02 16:03:30.441][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2025-08-02 16:03:30.442][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2025-08-02 16:03:30.443][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-02 16:03:30.444][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-02 16:03:30.445][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2025-08-02 16:03:30.445][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2025-08-02 16:03:30.446][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2025-08-02 16:03:30.447][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-02 16:03:30.448][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2025-08-02 16:03:30.449][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-02 16:03:30.450][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2025-08-02 16:03:30.451][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2025-08-02 16:03:30.452][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-02 16:03:30.453][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>". biodb.DEBUG[2025-08-02 16:03:30.454][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2025-08-02 16:03:30.455][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>". biodb.DEBUG[2025-08-02 16:03:30.456][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2025-08-02 16:03:30.457][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-02 16:03:30.457][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-02 16:03:30.458][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-02 16:03:30.459][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-02 16:03:30.460][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-02 16:03:30.461][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-02 16:03:30.462][self$setPropertyValue] Setting property "urls" to "<NULL>". biodb.DEBUG[2025-08-02 16:03:30.466][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-02 16:03:30.467][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-02 16:03:30.468][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2025-08-02 16:03:30.469][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-02 16:03:30.470][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-08-02 16:03:30.471][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.473][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.477][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.481][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.485][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.489][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.493][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.497][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.501][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.506][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.509][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[2025-08-02 16:03:30.510][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.514][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.518][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.522][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.526][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.530][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.533][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[2025-08-02 16:03:30.534][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.538][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[2025-08-02 16:03:30.538][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2025-08-02 16:03:30.540][self$getEntryFields()$define] Define field description. biodb.DEBUG[2025-08-02 16:03:30.541][self$getEntryFields()$define] Define field name. biodb.DEBUG[2025-08-02 16:03:30.542][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2025-08-02 16:03:30.544][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2025-08-02 16:03:30.545][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2025-08-02 16:03:30.546][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2025-08-02 16:03:30.547][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2025-08-02 16:03:30.549][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2025-08-02 16:03:30.550][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2025-08-02 16:03:30.551][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2025-08-02 16:03:30.553][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2025-08-02 16:03:30.554][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2025-08-02 16:03:30.555][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2025-08-02 16:03:30.556][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2025-08-02 16:03:30.558][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2025-08-02 16:03:30.559][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2025-08-02 16:03:30.560][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2025-08-02 16:03:30.562][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2025-08-02 16:03:30.563][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2025-08-02 16:03:30.564][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2025-08-02 16:03:30.565][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2025-08-02 16:03:30.567][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2025-08-02 16:03:30.568][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2025-08-02 16:03:30.569][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2025-08-02 16:03:30.571][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2025-08-02 16:03:30.572][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2025-08-02 16:03:30.573][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2025-08-02 16:03:30.574][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2025-08-02 16:03:30.576][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2025-08-02 16:03:30.577][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2025-08-02 16:03:30.578][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2025-08-02 16:03:30.580][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2025-08-02 16:03:30.585][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2025-08-02 16:03:30.586][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2025-08-02 16:03:30.587][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2025-08-02 16:03:30.588][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2025-08-02 16:03:30.590][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2025-08-02 16:03:30.591][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2025-08-02 16:03:30.592][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2025-08-02 16:03:30.593][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2025-08-02 16:03:30.595][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2025-08-02 16:03:30.596][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2025-08-02 16:03:30.597][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2025-08-02 16:03:30.599][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2025-08-02 16:03:30.600][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2025-08-02 16:03:30.601][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2025-08-02 16:03:30.602][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2025-08-02 16:03:30.604][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2025-08-02 16:03:30.605][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2025-08-02 16:03:30.606][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2025-08-02 16:03:30.608][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2025-08-02 16:03:30.609][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2025-08-02 16:03:30.610][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2025-08-02 16:03:30.611][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2025-08-02 16:03:30.613][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2025-08-02 16:03:30.614][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2025-08-02 16:03:30.615][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2025-08-02 16:03:30.617][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2025-08-02 16:03:30.618][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2025-08-02 16:03:30.619][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2025-08-02 16:03:30.620][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2025-08-02 16:03:30.622][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2025-08-02 16:03:30.623][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2025-08-02 16:03:30.624][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2025-08-02 16:03:30.626][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2025-08-02 16:03:30.627][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2025-08-02 16:03:30.628][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2025-08-02 16:03:30.629][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2025-08-02 16:03:30.631][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2025-08-02 16:03:30.632][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2025-08-02 16:03:30.633][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2025-08-02 16:03:30.635][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2025-08-02 16:03:30.636][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2025-08-02 16:03:30.637][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2025-08-02 16:03:30.638][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2025-08-02 16:03:30.640][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2025-08-02 16:03:30.641][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2025-08-02 16:03:30.642][self$getEntryFields()$define] Define field products. biodb.DEBUG[2025-08-02 16:03:30.643][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2025-08-02 16:03:30.645][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2025-08-02 16:03:30.646][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2025-08-02 16:03:30.647][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2025-08-02 16:03:30.649][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2025-08-02 16:03:30.650][initialize] This is biodb version 1.17.1. biodb.DEBUG[2025-08-02 16:03:30.651][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2025-08-02 16:03:30.652][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.653][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.655][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:30.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:30.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.661][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:30.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:30.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.667][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:30.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:30.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.672][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:30.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:30.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.678][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:30.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:30.681][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.684][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:30.686][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:30.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.690][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:30.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:30.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.695][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:30.697][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:30.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.705][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:30.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:30.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.711][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:30.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:30.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.717][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:30.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:30.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.722][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:30.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:30.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.728][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:30.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:30.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.734][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:30.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:30.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.740][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:30.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:30.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.746][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2025-08-02 16:03:30.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:30.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:30.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2025-08-02 16:03:30.752][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml". biodb.DEBUG[2025-08-02 16:03:30.753][self$getDbsInfo()$define] Define connector nci.cactus. biodb.DEBUG[2025-08-02 16:03:30.755][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2025-08-02 16:03:30.756][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.". biodb.DEBUG[2025-08-02 16:03:30.757][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2025-08-02 16:03:30.758][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2025-08-02 16:03:30.759][self$setPropertyValue] Setting property "downloadable" to "TRUE". biodb.DEBUG[2025-08-02 16:03:30.760][self$setPropertyValue] Setting property "dwnld.ext" to "gz". biodb.DEBUG[2025-08-02 16:03:30.761][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2025-08-02 16:03:30.762][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2025-08-02 16:03:30.762][self$setPropertyValue] Setting property "entry.content.type" to "sdf". biodb.DEBUG[2025-08-02 16:03:30.763][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2025-08-02 16:03:30.764][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2025-08-02 16:03:30.765][self$setPropertyValue] Setting property "name" to "NCI CACTUS". biodb.DEBUG[2025-08-02 16:03:30.766][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2025-08-02 16:03:30.767][self$setPropertyValue] Setting property "parsing.expr" to "NSC". biodb.DEBUG[2025-08-02 16:03:30.767][self$setPropertyValue] Setting property "parsing.expr" to "DTP names". biodb.DEBUG[2025-08-02 16:03:30.767][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI". biodb.DEBUG[2025-08-02 16:03:30.767][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")". biodb.DEBUG[2025-08-02 16:03:30.767][self$setPropertyValue] Setting property "parsing.expr" to "Formula". biodb.DEBUG[2025-08-02 16:03:30.767][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight". biodb.DEBUG[2025-08-02 16:03:30.767][self$setPropertyValue] Setting property "parsing.expr" to "CAS". biodb.DEBUG[2025-08-02 16:03:30.768][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2025-08-02 16:03:30.769][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>". biodb.DEBUG[2025-08-02 16:03:30.770][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2025-08-02 16:03:30.771][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-02 16:03:30.772][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-02 16:03:30.772][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2025-08-02 16:03:30.773][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2025-08-02 16:03:30.774][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2025-08-02 16:03:30.775][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2025-08-02 16:03:30.776][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/". biodb.DEBUG[2025-08-02 16:03:30.776][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/". biodb.DEBUG[2025-08-02 16:03:30.776][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/". biodb.DEBUG[2025-08-02 16:03:30.776][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz". biodb.DEBUG[2025-08-02 16:03:30.777][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2025-08-02 16:03:30.778][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2025-08-02 16:03:30.779][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2025-08-02 16:03:30.780][self$setPropertyValue] Setting property "xml.ns" to "<NULL>". biodb.DEBUG[2025-08-02 16:03:30.781][self$getEntryFields()$define] Define field nci.cactus.id. biodb.DEBUG[2025-08-02 16:03:30.784][super$initialize] Initialize connector nci.cactus. biodb.DEBUG[2025-08-02 16:03:30.787][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus . biodb.INFO [2025-08-02 16:03:30.788][biodb$terminate] Closing BiodbMain instance... biodb.INFO [2025-08-02 16:03:30.789][self$deleteConn] Connector "nci.cactus" deleted. biodb.DEBUG[2025-08-02 16:03:30.790][notifyObservers] Notify observers for terminate. biodb.DEBUG[2025-08-02 16:03:30.791][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2025-08-02 16:03:30.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2025-08-02 16:03:30.792][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2025-08-02 16:03:30.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2025-08-02 16:03:30.794][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2025-08-02 16:03:30.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". [ 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: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.13.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’ * checking for file ‘biodbNci/DESCRIPTION’ ... OK * this is package ‘biodbNci’ version ‘1.13.1’ * 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking installed package size ... INFO installed size is 6.1Mb sub-directories of 1Mb or more: libs 5.8Mb * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking 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 ‘/home/biocbuild/bbs-3.22-bioc-longtests/meat/biodbNci.Rcheck/00check.log’ for details.
biodbNci.Rcheck/00install.out
* installing *source* package ‘biodbNci’ ... ** this is package ‘biodbNci’ version ‘1.13.1’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c extractEntries.cpp -o extractEntries.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c test-100-example.cpp -o test-100-example.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c test-runner.cpp -o test-runner.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR installing to /home/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)