Back to Long Tests report for BioC 3.19 |
This page was generated on 2024-05-04 23:55:02 -0400 (Sat, 04 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4753 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" | 4486 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" | 4519 |
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 12/33 | Hostname | OS / Arch | CHECK | |||||||
biodbNci 1.8.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | |||||||
palomino3 | Windows Server 2022 Datacenter / x64 | ERROR | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ||||||||
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: 1.8.0 |
Command: /home/biocbuild/bbs-3.19-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_1.8.0.tar.gz |
StartedAt: 2024-05-04 16:09:09 -0400 (Sat, 04 May 2024) |
EndedAt: 2024-05-04 16:10:13 -0400 (Sat, 04 May 2024) |
EllapsedTime: 64.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: biodbNci.Rcheck |
Warnings: 0 |
biodbNci.Rcheck/tests/testthat.Rout
R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" Copyright (C) 2024 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) > Sys.setenv(TESTTHAT_REPORTER="summary") > Sys.setenv(BIODB_LOG_DST="console") > test_check("biodbNci") biodb.INFO [2024-05-04 16:10:10.409][biodb::testContext] biodb.INFO [2024-05-04 16:10:10.411][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 16:10:10.411][biodb::testContext] Test context - Generic long tests biodb.INFO [2024-05-04 16:10:10.412][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 16:10:10.413][biodb::testContext] biodb.INFO [2024-05-04 16:10:10.419][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0. biodb.DEBUG[2024-05-04 16:10:10.421][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml". biodb.DEBUG[2024-05-04 16:10:10.428][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 16:10:10.429][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2024-05-04 16:10:10.430][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2024-05-04 16:10:10.431][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.433][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2024-05-04 16:10:10.450][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2024-05-04 16:10:10.451][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.453][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2024-05-04 16:10:10.454][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2024-05-04 16:10:10.455][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.458][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2024-05-04 16:10:10.458][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2024-05-04 16:10:10.459][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2024-05-04 16:10:10.460][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.463][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2024-05-04 16:10:10.464][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2024-05-04 16:10:10.464][self$set] Set key cache.system to TRUE. biodb.DEBUG[2024-05-04 16:10:10.465][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.468][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2024-05-04 16:10:10.469][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2024-05-04 16:10:10.469][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.472][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2024-05-04 16:10:10.473][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2024-05-04 16:10:10.474][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2024-05-04 16:10:10.475][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.477][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2024-05-04 16:10:10.478][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2024-05-04 16:10:10.479][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.480][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[2024-05-04 16:10:10.481][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2024-05-04 16:10:10.482][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2024-05-04 16:10:10.483][self$set] Set key force.locale to TRUE. biodb.DEBUG[2024-05-04 16:10:10.484][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.486][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2024-05-04 16:10:10.487][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2024-05-04 16:10:10.488][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2024-05-04 16:10:10.489][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2024-05-04 16:10:10.490][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2024-05-04 16:10:10.491][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2024-05-04 16:10:10.492][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.494][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2024-05-04 16:10:10.495][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2024-05-04 16:10:10.496][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.498][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2024-05-04 16:10:10.499][self$set] Set key entries.sep to "|". biodb.DEBUG[2024-05-04 16:10:10.500][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.503][self$getConfig()$define] Define config key offline. biodb.DEBUG[2024-05-04 16:10:10.504][self$set] Set key offline to FALSE. biodb.DEBUG[2024-05-04 16:10:10.504][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.507][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2024-05-04 16:10:10.508][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2024-05-04 16:10:10.509][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.511][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2024-05-04 16:10:10.512][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2024-05-04 16:10:10.513][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.515][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2024-05-04 16:10:10.516][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2024-05-04 16:10:10.520][self$set] Set key svn.binary.path to "". biodb.DEBUG[2024-05-04 16:10:10.520][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.523][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2024-05-04 16:10:10.524][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2024-05-04 16:10:10.525][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2024-05-04 16:10:10.526][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.531][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2024-05-04 16:10:10.561][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 16:10:10.580][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2024-05-04 16:10:10.581][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:10:10.582][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:10:10.583][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:10:10.584][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:10:10.585][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:10:10.586][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:10:10.587][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 16:10:10.588][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:10:10.589][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 16:10:10.589][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2024-05-04 16:10:10.590][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:10:10.591][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:10:10.592][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:10:10.593][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 16:10:10.593][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 16:10:10.593][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 16:10:10.593][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 16:10:10.593][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 16:10:10.594][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:10:10.595][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:10:10.596][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:10:10.596][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:10:10.597][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:10:10.598][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:10:10.599][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:10:10.600][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:10:10.601][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:10:10.602][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:10:10.603][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:10:10.603][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:10:10.604][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2024-05-04 16:10:10.606][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 16:10:10.607][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 16:10:10.608][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:10:10.609][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:10:10.610][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:10:10.611][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:10:10.611][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:10:10.612][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:10:10.613][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 16:10:10.614][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:10:10.615][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 16:10:10.616][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2024-05-04 16:10:10.617][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:10:10.618][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:10:10.619][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:10:10.620][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 16:10:10.620][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 16:10:10.620][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 16:10:10.620][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 16:10:10.620][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 16:10:10.621][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:10:10.621][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:10:10.622][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:10:10.623][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:10:10.624][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:10:10.625][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:10:10.626][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:10:10.627][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:10:10.627][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:10:10.628][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:10:10.629][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:10:10.630][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:10:10.631][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2024-05-04 16:10:10.633][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 16:10:10.633][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2024-05-04 16:10:10.634][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:10:10.635][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:10:10.636][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:10:10.637][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:10:10.638][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:10:10.639][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:10:10.640][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 16:10:10.641][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:10:10.642][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 16:10:10.642][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2024-05-04 16:10:10.643][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:10:10.644][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:10:10.645][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:10:10.646][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:10:10.647][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:10:10.648][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:10:10.649][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:10:10.649][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:10:10.650][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:10:10.651][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:10:10.652][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:10:10.653][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:10:10.654][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:10:10.655][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:10:10.655][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:10:10.656][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:10:10.657][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2024-05-04 16:10:10.659][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 16:10:10.660][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 16:10:10.661][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:10:10.662][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:10:10.663][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:10:10.663][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:10:10.664][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:10:10.665][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:10:10.666][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 16:10:10.667][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:10:10.668][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 16:10:10.669][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2024-05-04 16:10:10.670][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:10:10.671][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:10:10.672][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:10:10.672][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:10:10.673][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:10:10.674][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:10:10.675][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:10:10.676][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:10:10.677][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:10:10.678][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:10:10.678][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:10:10.679][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:10:10.680][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:10:10.681][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:10:10.682][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:10:10.683][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:10:10.687][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 16:10:10.687][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.689][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:10.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:10.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.693][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:10.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:10.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.697][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:10.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:10.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.701][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:10.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:10.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.704][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[2024-05-04 16:10:10.705][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:10.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:10.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.709][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:10.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:10.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.713][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:10.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:10.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.717][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:10.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:10.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.721][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:10.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:10.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.729][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:10.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:10.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.733][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[2024-05-04 16:10:10.734][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:10.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:10.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.739][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:10.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:10.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.743][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:10.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:10.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.748][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:10.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:10.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.766][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:10.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:10.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.770][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:10.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:10.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.775][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:10.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:10.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.778][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[2024-05-04 16:10:10.779][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2024-05-04 16:10:10.784][self$getEntryFields()$define] Define field description. biodb.DEBUG[2024-05-04 16:10:10.786][self$getEntryFields()$define] Define field name. biodb.DEBUG[2024-05-04 16:10:10.787][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2024-05-04 16:10:10.789][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-05-04 16:10:10.790][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2024-05-04 16:10:10.792][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2024-05-04 16:10:10.793][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2024-05-04 16:10:10.794][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2024-05-04 16:10:10.796][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2024-05-04 16:10:10.797][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-05-04 16:10:10.798][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2024-05-04 16:10:10.800][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2024-05-04 16:10:10.801][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2024-05-04 16:10:10.803][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2024-05-04 16:10:10.804][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-04 16:10:10.805][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2024-05-04 16:10:10.807][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2024-05-04 16:10:10.808][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-05-04 16:10:10.809][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2024-05-04 16:10:10.811][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2024-05-04 16:10:10.812][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2024-05-04 16:10:10.813][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2024-05-04 16:10:10.815][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2024-05-04 16:10:10.816][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2024-05-04 16:10:10.818][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2024-05-04 16:10:10.819][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2024-05-04 16:10:10.820][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2024-05-04 16:10:10.822][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2024-05-04 16:10:10.823][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2024-05-04 16:10:10.824][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2024-05-04 16:10:10.826][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2024-05-04 16:10:10.827][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2024-05-04 16:10:10.828][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2024-05-04 16:10:10.830][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2024-05-04 16:10:10.831][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2024-05-04 16:10:10.833][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2024-05-04 16:10:10.834][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2024-05-04 16:10:10.835][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2024-05-04 16:10:10.837][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2024-05-04 16:10:10.838][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2024-05-04 16:10:10.839][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2024-05-04 16:10:10.841][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2024-05-04 16:10:10.842][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2024-05-04 16:10:10.843][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2024-05-04 16:10:10.845][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2024-05-04 16:10:10.846][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2024-05-04 16:10:10.848][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2024-05-04 16:10:10.849][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2024-05-04 16:10:10.850][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2024-05-04 16:10:10.852][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2024-05-04 16:10:10.853][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2024-05-04 16:10:10.854][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2024-05-04 16:10:10.856][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2024-05-04 16:10:10.857][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2024-05-04 16:10:10.858][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2024-05-04 16:10:10.860][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2024-05-04 16:10:10.861][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2024-05-04 16:10:10.862][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2024-05-04 16:10:10.864][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2024-05-04 16:10:10.865][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2024-05-04 16:10:10.866][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2024-05-04 16:10:10.868][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2024-05-04 16:10:10.869][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2024-05-04 16:10:10.870][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2024-05-04 16:10:10.872][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2024-05-04 16:10:10.873][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-05-04 16:10:10.874][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-05-04 16:10:10.876][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2024-05-04 16:10:10.877][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2024-05-04 16:10:10.878][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2024-05-04 16:10:10.880][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2024-05-04 16:10:10.881][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2024-05-04 16:10:10.883][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2024-05-04 16:10:10.884][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2024-05-04 16:10:10.885][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2024-05-04 16:10:10.887][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2024-05-04 16:10:10.888][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2024-05-04 16:10:10.889][self$getEntryFields()$define] Define field products. biodb.DEBUG[2024-05-04 16:10:10.891][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2024-05-04 16:10:10.892][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2024-05-04 16:10:10.893][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2024-05-04 16:10:10.895][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2024-05-04 16:10:10.900][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2024-05-04 16:10:10.902][initialize] This is biodb version 1.12.0. biodb.DEBUG[2024-05-04 16:10:10.905][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 16:10:10.906][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:10.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:10.908][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.913][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:10.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:10.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:10.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:10.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.919][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:10.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:10.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:10.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:10.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.925][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:10.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:10.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:10.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:10.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.930][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:10.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:10.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:10.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:10.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.941][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:10.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:10.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:10.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:10.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.946][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:10.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:10.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:10.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:10.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.952][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:10.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:10.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:10.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:10.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.957][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:10.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:10.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:10.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:10.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.963][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:10.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:10.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:10.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:10.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.968][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:10.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:10.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:10.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:10.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.974][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:10.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:10.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:10.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:10.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.980][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:10.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:10.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:10.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:10.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.985][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:10.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:10.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:10.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:10.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.991][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:10.992][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:10.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:10.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:10.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:10.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:10.996][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:10.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:10.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:10.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:11.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:11.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:11.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:11.002][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:11.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:11.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:11.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:11.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:11.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:11.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:11.008][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:11.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:11.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:11.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:11.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:11.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:11.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:11.014][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml". biodb.DEBUG[2024-05-04 16:10:11.023][self$getDbsInfo()$define] Define connector nci.cactus. biodb.DEBUG[2024-05-04 16:10:11.024][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 16:10:11.025][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.". biodb.DEBUG[2024-05-04 16:10:11.026][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:10:11.027][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:10:11.028][self$setPropertyValue] Setting property "downloadable" to "TRUE". biodb.DEBUG[2024-05-04 16:10:11.029][self$setPropertyValue] Setting property "dwnld.ext" to "gz". biodb.DEBUG[2024-05-04 16:10:11.030][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2024-05-04 16:10:11.031][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:10:11.031][self$setPropertyValue] Setting property "entry.content.type" to "sdf". biodb.DEBUG[2024-05-04 16:10:11.032][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:10:11.033][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 16:10:11.034][self$setPropertyValue] Setting property "name" to "NCI CACTUS". biodb.DEBUG[2024-05-04 16:10:11.035][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:10:11.036][self$setPropertyValue] Setting property "parsing.expr" to "NSC". biodb.DEBUG[2024-05-04 16:10:11.036][self$setPropertyValue] Setting property "parsing.expr" to "DTP names". biodb.DEBUG[2024-05-04 16:10:11.036][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI". biodb.DEBUG[2024-05-04 16:10:11.036][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")". biodb.DEBUG[2024-05-04 16:10:11.036][self$setPropertyValue] Setting property "parsing.expr" to "Formula". biodb.DEBUG[2024-05-04 16:10:11.036][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight". biodb.DEBUG[2024-05-04 16:10:11.036][self$setPropertyValue] Setting property "parsing.expr" to "CAS". biodb.DEBUG[2024-05-04 16:10:11.037][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2024-05-04 16:10:11.038][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:10:11.039][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2024-05-04 16:10:11.040][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:10:11.040][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:10:11.041][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:10:11.042][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:10:11.043][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:10:11.044][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:10:11.045][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/". biodb.DEBUG[2024-05-04 16:10:11.045][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/". biodb.DEBUG[2024-05-04 16:10:11.045][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/". biodb.DEBUG[2024-05-04 16:10:11.045][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz". biodb.DEBUG[2024-05-04 16:10:11.046][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:10:11.047][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:10:11.047][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2024-05-04 16:10:11.048][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:10:11.054][self$getEntryFields()$define] Define field nci.cactus.id. biodb.DEBUG[2024-05-04 16:10:11.077][super$initialize] Initialize connector nci.cactus. biodb.DEBUG[2024-05-04 16:10:11.078][super$initialize] Register connector nci.cactus with the request scheduler biodb.DEBUG[2024-05-04 16:10:11.082][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus. biodb.DEBUG[2024-05-04 16:10:11.086][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus". biodb.DEBUG[2024-05-04 16:10:11.091][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-04 16:10:11.092][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-04 16:10:11.093][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov". biodb.DEBUG[2024-05-04 16:10:11.094][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov". biodb.DEBUG[2024-05-04 16:10:11.095][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov". biodb.DEBUG[2024-05-04 16:10:11.096][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus . biodb.INFO [2024-05-04 16:10:11.106][biodb::testThat] biodb.INFO [2024-05-04 16:10:11.107][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value "). biodb.INFO [2024-05-04 16:10:11.107][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:10:11.108][biodb::testThat] biodb.TRACE[2024-05-04 16:10:11.112][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf". biodb.DEBUG[2024-05-04 16:10:11.114][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s). biodb.DEBUG[2024-05-04 16:10:11.117][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries. biodb.DEBUG[2024-05-04 16:10:11.157][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 16:10:11.158][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:11.159][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:11.171][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:11.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:11.173][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:11.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 16:10:11.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.194][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.209][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.211][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:10:11.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:10:11.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.214][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.238][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:10:11.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:10:11.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.242][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:10:11.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:10:11.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.245][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.246][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:10:11.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:10:11.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.249][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.251][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:10:11.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:10:11.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.254][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.255][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:10:11.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:10:11.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.259][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:10:11.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:10:11.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.261][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.262][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:10:11.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:10:11.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.265][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.267][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:11.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:11.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.270][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.271][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:11.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:11.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.273][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.277][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.278][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:11.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:11.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.281][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.282][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.285][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.289][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.293][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.335][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.339][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.343][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 16:10:11.344][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674. biodb.TRACE[2024-05-04 16:10:11.346][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:10:11.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:10:11.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.349][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.350][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:10:11.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:10:11.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.353][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.354][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-04 16:10:11.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-04 16:10:11.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.357][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.358][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-04 16:10:11.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-04 16:10:11.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.361][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.379][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.392][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:11.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:11.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.395][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.402][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.406][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.410][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.415][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.419][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.423][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.424][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:11.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:11.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.427][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.428][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:11.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:11.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.431][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.432][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:11.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:11.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.435][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.446][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.456][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.459][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.460][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.461][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.462][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.463][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.467][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.476][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:10:11.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:10:11.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.479][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.480][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:10:11.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:10:11.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.483][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.484][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:10:11.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:10:11.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.487][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.488][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:10:11.489][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:10:11.490][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.491][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.492][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:10:11.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:10:11.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.495][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.503][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:10:11.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:10:11.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.505][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.506][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:10:11.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:10:11.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.509][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.510][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:10:11.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:10:11.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.513][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.514][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:10:11.515][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:10:11.516][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.517][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.518][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:10:11.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:10:11.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.521][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.528][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:10:11.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:10:11.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.531][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.533][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:10:11.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:10:11.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.535][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.536][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:10:11.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:10:11.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.539][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.540][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:10:11.541][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:10:11.542][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.543][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.544][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:10:11.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:10:11.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.547][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.554][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:10:11.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:10:11.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.557][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.558][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:10:11.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:10:11.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.561][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.562][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:10:11.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:10:11.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.565][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.566][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:10:11.567][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:10:11.568][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.569][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.570][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:10:11.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:10:11.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.573][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.580][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.581][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.582][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.583][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.587][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:10:11.588][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:10:11.589][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.590][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.593][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:10:11.594][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:10:11.600][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.601][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.605][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:10:11.606][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:10:11.607][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.608][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.611][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:10:11.612][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:10:11.613][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.614][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.629][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf". biodb.DEBUG[2024-05-04 16:10:11.660][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s). biodb.DEBUG[2024-05-04 16:10:11.661][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries. biodb.DEBUG[2024-05-04 16:10:11.663][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 16:10:11.664][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:11.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:11.668][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:11.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:11.670][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:11.671][FUN] Functions in observer BiodbConfig: [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[2024-05-04 16:10:11.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.682][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.686][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.702][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-04 16:10:11.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-04 16:10:11.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.705][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.706][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-04 16:10:11.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-04 16:10:11.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.708][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.710][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:10:11.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:10:11.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.712][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.713][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:10:11.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:10:11.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.720][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.721][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:10:11.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:10:11.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.723][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.724][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:10:11.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:10:11.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.727][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.728][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:10:11.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:10:11.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.731][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.732][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:10:11.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:10:11.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.734][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.736][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:10:11.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:10:11.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.738][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.739][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:10:11.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:10:11.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.742][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.743][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:10:11.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:10:11.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.745][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.746][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:10:11.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:10:11.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.749][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.750][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:10:11.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:10:11.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.753][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.754][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:10:11.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:10:11.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.757][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.758][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:10:11.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:10:11.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.760][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.762][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:10:11.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:10:11.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.764][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.765][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:10:11.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:10:11.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.768][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.769][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:11.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:11.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.772][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.773][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:11.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:11.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.776][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.779][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.780][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:11.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:11.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.783][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.787][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.790][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.794][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.795][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.798][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.801][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.805][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 16:10:11.806][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690. biodb.TRACE[2024-05-04 16:10:11.824][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:10:11.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:10:11.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.827][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:10:11.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:10:11.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.830][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.831][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-04 16:10:11.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-04 16:10:11.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.834][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.835][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-04 16:10:11.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-04 16:10:11.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.837][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.842][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.849][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:11.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:11.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.852][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.858][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.862][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.865][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.870][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.874][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.877][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.878][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:11.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:11.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.881][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.882][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:11.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:11.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.885][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.886][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:11.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:11.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.888][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.905][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.909][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.913][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.914][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.914][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.915][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.916][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:11.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:11.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.920][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.927][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-04 16:10:11.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-04 16:10:11.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.929][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.930][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-04 16:10:11.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-04 16:10:11.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.933][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.934][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-04 16:10:11.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-04 16:10:11.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.937][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.937][ef$get] Asked field names are: cas.id. biodb.TRACE[2024-05-04 16:10:11.938][ef$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-04 16:10:11.939][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.940][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.941][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-04 16:10:11.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-04 16:10:11.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.950][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:10:11.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:10:11.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.953][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.954][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:10:11.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:10:11.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.957][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.958][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:10:11.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:10:11.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.960][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.961][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:10:11.962][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:10:11.963][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.964][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.965][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:10:11.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:10:11.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.974][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:10:11.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:10:11.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.981][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.981][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:10:11.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:10:11.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.984][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.985][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:10:11.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:10:11.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.988][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.989][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:10:11.989][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:10:11.990][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.991][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:11.992][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:10:11.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:10:11.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:11.995][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.002][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:10:12.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:10:12.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.004][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.005][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:10:12.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:10:12.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.008][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.009][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:10:12.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:10:12.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.012][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.013][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:10:12.013][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:10:12.014][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.015][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.016][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:10:12.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:10:12.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.019][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.026][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:10:12.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:10:12.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.028][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.029][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:10:12.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:10:12.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.032][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.033][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:10:12.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:10:12.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.035][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.036][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:10:12.037][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:10:12.038][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.039][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.040][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:10:12.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:10:12.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.043][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.049][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:10:12.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:10:12.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.052][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.053][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:10:12.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:10:12.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.056][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.056][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:10:12.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:10:12.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.059][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.060][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:10:12.061][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:10:12.062][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.063][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.064][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:10:12.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:10:12.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.066][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.073][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:12.074][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:12.075][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.076][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.079][ef$get] Asked field names are: cas.id. biodb.TRACE[2024-05-04 16:10:12.080][ef$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-04 16:10:12.081][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.082][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.085][ef$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:10:12.086][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:10:12.087][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.088][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.092][ef$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:10:12.093][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:10:12.094][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.094][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.098][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:10:12.099][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:10:12.100][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.101][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.104][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:10:12.109][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:10:12.110][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.110][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.114][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:10:12.115][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:10:12.116][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.116][ef$get] fields variable is a list. biodb.INFO [2024-05-04 16:10:12.122][biodb::testThat] biodb.INFO [2024-05-04 16:10:12.123][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. "). biodb.INFO [2024-05-04 16:10:12.124][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:10:12.125][biodb::testThat] biodb.DEBUG[2024-05-04 16:10:12.127][private$loadEntries] Creating entries from ids [2]: "749674, 750690". biodb.DEBUG[2024-05-04 16:10:12.134][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)... biodb.DEBUG[2024-05-04 16:10:12.138][self$isDownloaded] Database nci.cactus has already been downloaded. biodb.DEBUG[2024-05-04 16:10:12.139][self$isDownloaded] Database nci.cactus has already been downloaded. biodb.TRACE[2024-05-04 16:10:12.141][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690". biodb.TRACE[2024-05-04 16:10:12.142][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE". biodb.TRACE[2024-05-04 16:10:12.144][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, /home/biocbuild/.cache/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf". biodb.DEBUG[2024-05-04 16:10:12.145][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 16:10:12.146][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s). biodb.DEBUG[2024-05-04 16:10:12.147][self$createEntryFromContent] Parsing 2 NCI CACTUS entries. biodb.DEBUG[2024-05-04 16:10:12.149][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 16:10:12.149][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:12.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:12.154][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:12.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:12.156][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 16:10:12.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:12.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:12.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.165][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:12.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:12.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.168][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.171][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:10:12.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:10:12.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.173][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.174][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:10:12.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:10:12.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.177][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.178][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:10:12.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:10:12.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.181][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.182][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:10:12.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:10:12.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.184][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.186][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:10:12.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:10:12.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.189][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.190][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:10:12.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:10:12.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.192][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.194][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:10:12.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:10:12.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.196][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.197][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:10:12.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:10:12.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.200][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.201][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:12.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:12.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.204][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.205][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:12.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:12.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.208][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:12.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:12.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.211][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.212][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:12.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:12.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.215][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:12.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:12.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.218][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:12.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:12.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.222][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:12.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:12.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.225][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 16:10:12.226][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 16:10:12.227][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:12.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:12.232][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:12.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:12.233][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 16:10:12.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:12.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:12.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.245][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:12.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:12.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.253][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.255][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-04 16:10:12.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-04 16:10:12.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.258][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id. biodb.TRACE[2024-05-04 16:10:12.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id. biodb.TRACE[2024-05-04 16:10:12.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.261][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.262][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:10:12.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:10:12.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.265][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.266][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-05-04 16:10:12.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-05-04 16:10:12.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.269][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.270][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:10:12.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:10:12.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.273][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.273][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-05-04 16:10:12.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-05-04 16:10:12.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.276][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.277][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:10:12.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:10:12.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.280][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.281][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:10:12.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:10:12.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.284][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.285][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:10:12.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:10:12.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.287][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.288][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:10:12.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:10:12.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.291][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.292][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:10:12.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:10:12.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.295][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.295][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:10:12.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:10:12.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.298][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.299][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:10:12.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:10:12.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.302][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.303][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:10:12.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:10:12.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.306][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.307][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-05-04 16:10:12.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-05-04 16:10:12.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.310][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.311][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:10:12.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:10:12.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.314][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.314][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-05-04 16:10:12.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-05-04 16:10:12.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.317][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.319][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:12.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:12.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.321][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.322][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:12.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:12.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.325][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:12.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:12.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.328][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.329][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:12.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id. biodb.TRACE[2024-05-04 16:10:12.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.332][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:12.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:12.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.336][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:12.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:12.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.339][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:12.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:12.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.343][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:12.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:12.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.346][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:12.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:12.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.350][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:12.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:12.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.354][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:12.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:12.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.357][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:12.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:12.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.361][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:10:12.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:10:12.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.364][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 16:10:12.365][self$createEntryFromContent] Accession numbers: 749674, 750690. biodb.TRACE[2024-05-04 16:10:12.366][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt. biodb.TRACE[2024-05-04 16:10:12.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt. biodb.TRACE[2024-05-04 16:10:12.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.369][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.370][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min. biodb.TRACE[2024-05-04 16:10:12.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min. biodb.TRACE[2024-05-04 16:10:12.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.372][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.373][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max. biodb.TRACE[2024-05-04 16:10:12.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max. biodb.TRACE[2024-05-04 16:10:12.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.376][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.384][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt. biodb.TRACE[2024-05-04 16:10:12.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt. biodb.TRACE[2024-05-04 16:10:12.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.386][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.387][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min. biodb.TRACE[2024-05-04 16:10:12.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min. biodb.TRACE[2024-05-04 16:10:12.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.390][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.391][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max. biodb.TRACE[2024-05-04 16:10:12.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max. biodb.TRACE[2024-05-04 16:10:12.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.393][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-05-04 16:10:12.400][biodb::testThat] biodb.INFO [2024-05-04 16:10:12.401][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field "). biodb.INFO [2024-05-04 16:10:12.401][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:10:12.402][biodb::testThat] biodb.INFO [2024-05-04 16:10:12.407][biodb::testThat] biodb.INFO [2024-05-04 16:10:12.408][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. "). biodb.INFO [2024-05-04 16:10:12.409][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:10:12.410][biodb::testThat] biodb.WARN [2024-05-04 16:10:12.428][self$searchForEntries] This database is not searchable by field "name". biodb.WARN [2024-05-04 16:10:12.445][self$searchForEntries] This database is not searchable by field "name". biodb.INFO [2024-05-04 16:10:12.452][biodb::testThat] biodb.INFO [2024-05-04 16:10:12.453][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. "). biodb.INFO [2024-05-04 16:10:12.454][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:10:12.455][biodb::testThat] biodb.TRACE[2024-05-04 16:10:12.474][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:10:12.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:10:12.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.477][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.478][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:10:12.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:10:12.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.481][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.481][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-04 16:10:12.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-04 16:10:12.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.484][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.485][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-04 16:10:12.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-04 16:10:12.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.488][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.521][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:10:12.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:10:12.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.524][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.525][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:10:12.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:10:12.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.527][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.528][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-04 16:10:12.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-04 16:10:12.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.531][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:10:12.532][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-04 16:10:12.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-04 16:10:12.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:10:12.534][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-05-04 16:10:12.539][biodb::testThat] biodb.INFO [2024-05-04 16:10:12.540][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. "). biodb.INFO [2024-05-04 16:10:12.541][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:10:12.542][biodb::testThat] biodb.INFO [2024-05-04 16:10:12.548][biodb::testThat] biodb.INFO [2024-05-04 16:10:12.549][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. "). biodb.INFO [2024-05-04 16:10:12.550][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:10:12.550][biodb::testThat] biodb.INFO [2024-05-04 16:10:12.556][biodb::testThat] biodb.INFO [2024-05-04 16:10:12.557][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. "). biodb.INFO [2024-05-04 16:10:12.558][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:10:12.559][biodb::testThat] biodb.INFO [2024-05-04 16:10:12.564][biodb::testThat] biodb.INFO [2024-05-04 16:10:12.564][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. "). biodb.INFO [2024-05-04 16:10:12.565][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:10:12.566][biodb::testThat] biodb.INFO [2024-05-04 16:10:12.571][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2024-05-04 16:10:12.572][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler biodb.INFO [2024-05-04 16:10:12.573][self$deleteConn] Connector "nci.cactus" deleted. biodb.DEBUG[2024-05-04 16:10:12.574][notifyObservers] Notify observers for terminate. biodb.DEBUG[2024-05-04 16:10:12.574][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:12.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:12.576][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:12.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:12.578][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.579][FUN] Functions in observer BiodbConfig: [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 [2024-05-04 16:10:12.587][biodb::testContext] biodb.INFO [2024-05-04 16:10:12.587][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 16:10:12.588][biodb::testContext] Test context - Example long tests biodb.INFO [2024-05-04 16:10:12.589][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 16:10:12.590][biodb::testContext] biodb.INFO [2024-05-04 16:10:12.592][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0. biodb.DEBUG[2024-05-04 16:10:12.593][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc/R/site-library/biodb/definitions.yml". biodb.DEBUG[2024-05-04 16:10:12.597][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 16:10:12.598][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2024-05-04 16:10:12.599][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2024-05-04 16:10:12.599][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:12.602][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2024-05-04 16:10:12.603][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2024-05-04 16:10:12.604][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:12.606][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2024-05-04 16:10:12.607][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2024-05-04 16:10:12.608][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:12.610][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2024-05-04 16:10:12.611][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2024-05-04 16:10:12.612][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2024-05-04 16:10:12.613][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.615][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[2024-05-04 16:10:12.615][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2024-05-04 16:10:12.620][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2024-05-04 16:10:12.621][self$set] Set key cache.system to TRUE. biodb.DEBUG[2024-05-04 16:10:12.622][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:12.624][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2024-05-04 16:10:12.625][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2024-05-04 16:10:12.626][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:12.629][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2024-05-04 16:10:12.629][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2024-05-04 16:10:12.630][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2024-05-04 16:10:12.631][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:12.634][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2024-05-04 16:10:12.635][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2024-05-04 16:10:12.635][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:12.638][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2024-05-04 16:10:12.639][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2024-05-04 16:10:12.640][self$set] Set key force.locale to TRUE. biodb.DEBUG[2024-05-04 16:10:12.641][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:12.643][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2024-05-04 16:10:12.644][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2024-05-04 16:10:12.645][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2024-05-04 16:10:12.646][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2024-05-04 16:10:12.647][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2024-05-04 16:10:12.648][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2024-05-04 16:10:12.648][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:12.651][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2024-05-04 16:10:12.652][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2024-05-04 16:10:12.653][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:12.655][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2024-05-04 16:10:12.656][self$set] Set key entries.sep to "|". biodb.DEBUG[2024-05-04 16:10:12.657][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:12.659][self$getConfig()$define] Define config key offline. biodb.DEBUG[2024-05-04 16:10:12.660][self$set] Set key offline to FALSE. biodb.DEBUG[2024-05-04 16:10:12.661][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:12.663][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2024-05-04 16:10:12.664][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2024-05-04 16:10:12.665][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:12.668][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2024-05-04 16:10:12.669][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2024-05-04 16:10:12.669][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:12.672][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2024-05-04 16:10:12.673][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2024-05-04 16:10:12.676][self$set] Set key svn.binary.path to "". biodb.DEBUG[2024-05-04 16:10:12.677][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:12.679][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2024-05-04 16:10:12.680][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2024-05-04 16:10:12.681][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2024-05-04 16:10:12.682][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:12.684][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2024-05-04 16:10:12.686][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 16:10:12.687][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2024-05-04 16:10:12.688][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:10:12.689][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:10:12.690][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:10:12.690][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:10:12.691][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:10:12.692][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:10:12.693][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 16:10:12.694][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:10:12.695][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 16:10:12.696][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2024-05-04 16:10:12.697][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:10:12.698][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:10:12.699][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:10:12.699][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 16:10:12.699][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 16:10:12.699][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 16:10:12.699][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 16:10:12.699][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 16:10:12.700][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:10:12.701][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:10:12.702][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:10:12.703][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:10:12.704][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:10:12.705][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:10:12.706][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:10:12.706][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:10:12.707][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:10:12.708][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:10:12.709][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:10:12.710][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:10:12.711][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2024-05-04 16:10:12.712][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 16:10:12.713][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 16:10:12.714][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:10:12.715][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:10:12.716][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:10:12.717][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:10:12.718][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:10:12.719][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:10:12.720][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 16:10:12.721][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:10:12.721][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 16:10:12.722][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2024-05-04 16:10:12.723][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:10:12.724][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:10:12.725][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:10:12.726][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 16:10:12.726][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 16:10:12.726][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 16:10:12.726][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 16:10:12.726][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 16:10:12.727][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:10:12.728][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:10:12.729][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:10:12.729][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:10:12.730][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:10:12.731][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:10:12.732][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:10:12.736][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:10:12.737][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:10:12.738][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:10:12.739][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:10:12.740][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:10:12.742][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2024-05-04 16:10:12.744][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 16:10:12.745][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2024-05-04 16:10:12.746][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:10:12.747][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:10:12.748][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:10:12.749][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:10:12.764][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:10:12.765][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:10:12.766][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 16:10:12.767][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:10:12.768][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 16:10:12.769][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2024-05-04 16:10:12.770][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:10:12.771][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:10:12.772][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:10:12.773][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:10:12.774][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:10:12.775][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:10:12.776][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:10:12.777][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:10:12.778][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:10:12.779][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:10:12.780][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:10:12.781][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:10:12.782][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:10:12.783][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:10:12.784][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:10:12.785][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:10:12.786][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2024-05-04 16:10:12.787][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 16:10:12.788][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 16:10:12.789][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:10:12.790][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:10:12.791][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:10:12.792][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:10:12.793][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:10:12.794][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:10:12.795][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 16:10:12.796][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:10:12.797][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 16:10:12.798][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2024-05-04 16:10:12.799][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:10:12.800][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:10:12.801][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:10:12.802][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:10:12.803][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:10:12.804][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:10:12.805][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:10:12.806][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:10:12.807][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:10:12.808][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:10:12.809][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:10:12.809][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:10:12.810][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:10:12.811][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:10:12.812][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:10:12.813][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:10:12.814][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 16:10:12.815][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:12.817][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:12.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:12.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:12.821][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:12.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:12.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.825][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[2024-05-04 16:10:12.826][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:12.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:12.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:12.830][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:12.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:12.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.834][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[2024-05-04 16:10:12.834][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:12.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:12.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:12.839][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:12.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:12.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:12.843][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:12.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:12.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.847][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[2024-05-04 16:10:12.848][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:12.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:12.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:12.852][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:12.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:12.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:12.856][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:12.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:12.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:12.861][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:12.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:12.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:12.865][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:12.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:12.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:12.869][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:12.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:12.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:12.874][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:12.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:12.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:12.878][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:12.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:12.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:12.882][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:12.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:12.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:12.886][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:12.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:12.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:12.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:12.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:12.890][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2024-05-04 16:10:12.892][self$getEntryFields()$define] Define field description. biodb.DEBUG[2024-05-04 16:10:12.893][self$getEntryFields()$define] Define field name. biodb.DEBUG[2024-05-04 16:10:12.898][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2024-05-04 16:10:12.899][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-05-04 16:10:12.900][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2024-05-04 16:10:12.902][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2024-05-04 16:10:12.903][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2024-05-04 16:10:12.904][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2024-05-04 16:10:12.905][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2024-05-04 16:10:12.906][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-05-04 16:10:12.908][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2024-05-04 16:10:12.909][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2024-05-04 16:10:12.910][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2024-05-04 16:10:12.911][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2024-05-04 16:10:12.913][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-04 16:10:12.914][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2024-05-04 16:10:12.915][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2024-05-04 16:10:12.916][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-05-04 16:10:12.918][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2024-05-04 16:10:12.919][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2024-05-04 16:10:12.920][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2024-05-04 16:10:12.922][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2024-05-04 16:10:12.923][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2024-05-04 16:10:12.924][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2024-05-04 16:10:12.925][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2024-05-04 16:10:12.927][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2024-05-04 16:10:12.928][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2024-05-04 16:10:12.929][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2024-05-04 16:10:12.930][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2024-05-04 16:10:12.932][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2024-05-04 16:10:12.933][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2024-05-04 16:10:12.934][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2024-05-04 16:10:12.935][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2024-05-04 16:10:12.937][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2024-05-04 16:10:12.938][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2024-05-04 16:10:12.939][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2024-05-04 16:10:12.940][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2024-05-04 16:10:12.942][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2024-05-04 16:10:12.943][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2024-05-04 16:10:12.944][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2024-05-04 16:10:12.945][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2024-05-04 16:10:12.946][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2024-05-04 16:10:12.948][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2024-05-04 16:10:12.949][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2024-05-04 16:10:12.950][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2024-05-04 16:10:12.952][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2024-05-04 16:10:12.953][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2024-05-04 16:10:12.954][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2024-05-04 16:10:12.955][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2024-05-04 16:10:12.957][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2024-05-04 16:10:12.958][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2024-05-04 16:10:12.959][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2024-05-04 16:10:12.960][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2024-05-04 16:10:12.962][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2024-05-04 16:10:12.963][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2024-05-04 16:10:12.964][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2024-05-04 16:10:12.965][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2024-05-04 16:10:12.967][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2024-05-04 16:10:12.968][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2024-05-04 16:10:12.969][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2024-05-04 16:10:12.970][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2024-05-04 16:10:12.972][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2024-05-04 16:10:12.973][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2024-05-04 16:10:12.974][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2024-05-04 16:10:12.975][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2024-05-04 16:10:12.977][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-05-04 16:10:12.978][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-05-04 16:10:12.979][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2024-05-04 16:10:12.980][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2024-05-04 16:10:12.982][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2024-05-04 16:10:12.983][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2024-05-04 16:10:12.984][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2024-05-04 16:10:12.985][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2024-05-04 16:10:12.987][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2024-05-04 16:10:12.988][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2024-05-04 16:10:12.989][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2024-05-04 16:10:12.990][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2024-05-04 16:10:12.992][self$getEntryFields()$define] Define field products. biodb.DEBUG[2024-05-04 16:10:12.993][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2024-05-04 16:10:12.994][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2024-05-04 16:10:12.995][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2024-05-04 16:10:12.997][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2024-05-04 16:10:12.998][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2024-05-04 16:10:13.000][initialize] This is biodb version 1.12.0. biodb.DEBUG[2024-05-04 16:10:13.001][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 16:10:13.001][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:13.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:13.003][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:13.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:13.005][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:13.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:13.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:13.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:13.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:13.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:13.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:13.010][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:13.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:13.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:13.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:13.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:13.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:13.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:13.016][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:13.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:13.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:13.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:13.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:13.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:13.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:13.026][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:13.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:13.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:13.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:13.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:13.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:13.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:13.031][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:13.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:13.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:13.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:13.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:13.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:13.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:13.037][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:13.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:13.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:13.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:13.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:13.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:13.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:13.042][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:13.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:13.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:13.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:13.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:13.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:13.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:13.048][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:13.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:13.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:13.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:13.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:13.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:13.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:13.054][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:13.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:13.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:13.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:13.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:13.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:13.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:13.059][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:13.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:13.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:13.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:13.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:13.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:13.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:13.065][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:13.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:13.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:13.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:13.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:13.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:13.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:13.070][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:13.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:13.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:13.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:13.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:13.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:13.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:13.076][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:13.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:13.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:13.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:13.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:13.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:13.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:13.082][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:13.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:13.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:13.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:13.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:13.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:13.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:13.087][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:13.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:13.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:13.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:13.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:13.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:13.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:13.093][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:13.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:13.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:13.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:13.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:13.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:13.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:13.099][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:10:13.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:13.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:13.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:13.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:13.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:13.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:10:13.105][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml". biodb.DEBUG[2024-05-04 16:10:13.106][self$getDbsInfo()$define] Define connector nci.cactus. biodb.DEBUG[2024-05-04 16:10:13.108][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 16:10:13.109][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.". biodb.DEBUG[2024-05-04 16:10:13.110][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:10:13.111][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:10:13.112][self$setPropertyValue] Setting property "downloadable" to "TRUE". biodb.DEBUG[2024-05-04 16:10:13.112][self$setPropertyValue] Setting property "dwnld.ext" to "gz". biodb.DEBUG[2024-05-04 16:10:13.113][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2024-05-04 16:10:13.114][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:10:13.115][self$setPropertyValue] Setting property "entry.content.type" to "sdf". biodb.DEBUG[2024-05-04 16:10:13.116][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:10:13.117][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 16:10:13.118][self$setPropertyValue] Setting property "name" to "NCI CACTUS". biodb.DEBUG[2024-05-04 16:10:13.119][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:10:13.120][self$setPropertyValue] Setting property "parsing.expr" to "NSC". biodb.DEBUG[2024-05-04 16:10:13.120][self$setPropertyValue] Setting property "parsing.expr" to "DTP names". biodb.DEBUG[2024-05-04 16:10:13.120][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI". biodb.DEBUG[2024-05-04 16:10:13.120][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")". biodb.DEBUG[2024-05-04 16:10:13.120][self$setPropertyValue] Setting property "parsing.expr" to "Formula". biodb.DEBUG[2024-05-04 16:10:13.120][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight". biodb.DEBUG[2024-05-04 16:10:13.120][self$setPropertyValue] Setting property "parsing.expr" to "CAS". biodb.DEBUG[2024-05-04 16:10:13.121][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2024-05-04 16:10:13.121][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:10:13.122][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2024-05-04 16:10:13.123][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:10:13.124][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:10:13.125][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:10:13.126][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:10:13.127][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:10:13.127][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:10:13.128][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/". biodb.DEBUG[2024-05-04 16:10:13.128][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/". biodb.DEBUG[2024-05-04 16:10:13.128][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/". biodb.DEBUG[2024-05-04 16:10:13.128][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz". biodb.DEBUG[2024-05-04 16:10:13.129][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:10:13.130][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:10:13.131][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2024-05-04 16:10:13.132][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:10:13.133][self$getEntryFields()$define] Define field nci.cactus.id. biodb.DEBUG[2024-05-04 16:10:13.136][super$initialize] Initialize connector nci.cactus. biodb.DEBUG[2024-05-04 16:10:13.137][super$initialize] Register connector nci.cactus with the request scheduler biodb.DEBUG[2024-05-04 16:10:13.138][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus. biodb.DEBUG[2024-05-04 16:10:13.139][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus". biodb.DEBUG[2024-05-04 16:10:13.144][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-04 16:10:13.145][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-04 16:10:13.146][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov". biodb.DEBUG[2024-05-04 16:10:13.148][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov". biodb.DEBUG[2024-05-04 16:10:13.149][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov". biodb.DEBUG[2024-05-04 16:10:13.150][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus . biodb.INFO [2024-05-04 16:10:13.151][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2024-05-04 16:10:13.152][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler biodb.INFO [2024-05-04 16:10:13.152][self$deleteConn] Connector "nci.cactus" deleted. biodb.DEBUG[2024-05-04 16:10:13.153][notifyObservers] Notify observers for terminate. biodb.DEBUG[2024-05-04 16:10:13.154][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:10:13.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:10:13.156][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:10:13.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:10:13.157][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:10:13.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". [ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ] > > proc.time() user system elapsed 4.211 0.269 4.467
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-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_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbNci.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 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 ‘1.8.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘biodbNci’ can be installed ... OK * used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... 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 ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... SKIPPED * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... OK * checking files in ‘vignettes’ ... SKIPPED * checking examples ... SKIPPED * checking for unstated dependencies in ‘longtests’ ... OK * checking tests in ‘longtests’ ... Running ‘testthat.R’ OK * DONE Status: OK
biodbNci.Rcheck/00install.out
* installing *source* package ‘biodbNci’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c extractEntries.cpp -o extractEntries.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-100-example.cpp -o test-100-example.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/testthat/include' -I/usr/local/include -fpic -g -O2 -Wall -c test-runner.cpp -o test-runner.o g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-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-3.19-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.19-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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbNci)