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 7/33 | Hostname | OS / Arch | CHECK | |||||||
biodbExpasy 1.8.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | |||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ||||||||
To the developers/maintainers of the biodbExpasy 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: biodbExpasy |
Version: 1.8.0 |
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.8.0.tar.gz |
StartedAt: 2024-05-04 16:04:49 -0400 (Sat, 04 May 2024) |
EndedAt: 2024-05-04 16:05:45 -0400 (Sat, 04 May 2024) |
EllapsedTime: 56.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: biodbExpasy.Rcheck |
Warnings: 0 |
biodbExpasy.Rcheck/tests/testthat.Rout
R version 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # Script needed to run testthat automatically from ‘R CMD check’. See > # testthat::test_dir documentation. > library(testthat) > library(biodbExpasy) > Sys.setenv(TESTTHAT_REPORTER="summary") > Sys.setenv(BIODB_LOG_DST="console") > test_check("biodbExpasy") biodb.INFO [2024-05-04 16:05:31.943][biodb::testContext] biodb.INFO [2024-05-04 16:05:31.946][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 16:05:31.948][biodb::testContext] Test context - Generic long tests biodb.INFO [2024-05-04 16:05:31.949][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 16:05:31.950][biodb::testContext] biodb.INFO [2024-05-04 16:05:31.958][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0. biodb.DEBUG[2024-05-04 16:05:31.961][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml". biodb.DEBUG[2024-05-04 16:05:31.999][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 16:05:32.001][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2024-05-04 16:05:32.003][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2024-05-04 16:05:32.004][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:32.008][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2024-05-04 16:05:32.041][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2024-05-04 16:05:32.042][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.044][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:32.046][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2024-05-04 16:05:32.047][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2024-05-04 16:05:32.048][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:32.051][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2024-05-04 16:05:32.053][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2024-05-04 16:05:32.054][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2024-05-04 16:05:32.055][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.057][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:32.058][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2024-05-04 16:05:32.060][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2024-05-04 16:05:32.061][self$set] Set key cache.system to TRUE. biodb.DEBUG[2024-05-04 16:05:32.062][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:32.065][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2024-05-04 16:05:32.067][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2024-05-04 16:05:32.068][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.070][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 16:05:32.071][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2024-05-04 16:05:32.072][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2024-05-04 16:05:32.074][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2024-05-04 16:05:32.075][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:32.078][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2024-05-04 16:05:32.079][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2024-05-04 16:05:32.081][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.083][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:32.084][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2024-05-04 16:05:32.085][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2024-05-04 16:05:32.086][self$set] Set key force.locale to TRUE. biodb.DEBUG[2024-05-04 16:05:32.088][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:32.091][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2024-05-04 16:05:32.092][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2024-05-04 16:05:32.093][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2024-05-04 16:05:32.095][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2024-05-04 16:05:32.096][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2024-05-04 16:05:32.097][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2024-05-04 16:05:32.098][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.100][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:32.102][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2024-05-04 16:05:32.103][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2024-05-04 16:05:32.104][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:32.107][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2024-05-04 16:05:32.109][self$set] Set key entries.sep to "|". biodb.DEBUG[2024-05-04 16:05:32.110][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.112][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:32.113][self$getConfig()$define] Define config key offline. biodb.DEBUG[2024-05-04 16:05:32.114][self$set] Set key offline to FALSE. biodb.DEBUG[2024-05-04 16:05:32.115][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:32.119][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2024-05-04 16:05:32.120][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2024-05-04 16:05:32.121][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.123][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:32.124][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2024-05-04 16:05:32.126][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2024-05-04 16:05:32.127][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:32.130][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2024-05-04 16:05:32.132][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2024-05-04 16:05:32.135][self$set] Set key svn.binary.path to "". biodb.DEBUG[2024-05-04 16:05:32.137][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.139][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:32.140][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2024-05-04 16:05:32.141][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2024-05-04 16:05:32.143][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2024-05-04 16:05:32.144][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:32.149][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2024-05-04 16:05:32.176][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 16:05:32.190][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2024-05-04 16:05:32.192][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:05:32.193][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:05:32.194][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:05:32.195][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:05:32.197][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:05:32.198][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:05:32.199][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 16:05:32.200][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:05:32.202][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 16:05:32.203][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2024-05-04 16:05:32.204][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:05:32.205][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:05:32.206][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:05:32.208][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 16:05:32.208][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 16:05:32.208][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 16:05:32.208][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 16:05:32.208][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 16:05:32.209][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:05:32.210][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:05:32.211][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:05:32.212][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:05:32.214][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:05:32.215][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:05:32.216][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:05:32.217][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:05:32.218][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:05:32.219][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:05:32.221][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:05:32.222][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:05:32.229][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2024-05-04 16:05:32.231][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 16:05:32.232][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 16:05:32.233][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:05:32.235][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:05:32.236][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:05:32.237][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:05:32.238][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:05:32.239][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:05:32.241][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 16:05:32.242][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:05:32.243][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 16:05:32.244][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2024-05-04 16:05:32.245][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:05:32.247][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:05:32.248][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:05:32.249][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 16:05:32.249][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 16:05:32.249][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 16:05:32.249][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 16:05:32.249][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 16:05:32.250][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:05:32.251][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:05:32.252][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:05:32.254][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:05:32.255][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:05:32.256][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:05:32.257][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:05:32.258][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:05:32.259][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:05:32.260][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:05:32.262][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:05:32.263][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:05:32.264][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2024-05-04 16:05:32.266][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 16:05:32.267][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2024-05-04 16:05:32.269][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:05:32.270][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:05:32.271][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:05:32.272][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:05:32.273][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:05:32.275][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:05:32.276][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 16:05:32.277][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:05:32.279][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 16:05:32.280][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2024-05-04 16:05:32.281][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:05:32.282][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:05:32.283][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:05:32.285][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:05:32.286][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:05:32.287][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:05:32.288][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:05:32.289][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:05:32.290][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:05:32.291][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:05:32.293][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:05:32.294][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:05:32.295][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:05:32.296][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:05:32.297][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:05:32.298][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:05:32.300][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2024-05-04 16:05:32.302][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 16:05:32.303][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 16:05:32.304][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:05:32.305][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:05:32.307][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:05:32.308][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:05:32.309][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:05:32.310][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:05:32.311][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 16:05:32.313][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:05:32.314][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 16:05:32.315][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2024-05-04 16:05:32.316][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:05:32.318][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:05:32.319][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:05:32.320][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:05:32.321][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:05:32.322][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:05:32.323][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:05:32.325][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:05:32.326][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:05:32.327][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:05:32.328][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:05:32.329][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:05:32.330][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:05:32.332][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:05:32.333][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:05:32.334][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:05:32.338][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 16:05:32.339][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.340][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:32.341][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.343][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 16:05:32.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:32.347][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.349][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 16:05:32.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:32.352][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:05:32.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:32.358][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:05:32.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.362][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:32.363][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.365][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 16:05:32.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.368][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:32.369][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.371][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 16:05:32.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.373][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:32.374][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:05:32.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:32.380][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.382][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 16:05:32.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.384][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:32.385][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:05:32.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:32.391][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.393][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 16:05:32.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.395][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:32.396][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.398][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 16:05:32.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.401][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:32.402][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.404][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 16:05:32.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.406][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:32.407][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.409][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 16:05:32.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.412][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:32.413][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:05:32.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:32.418][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.420][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 16:05:32.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.423][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:32.424][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.426][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 16:05:32.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:32.429][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.431][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 16:05:32.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.434][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:32.435][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2024-05-04 16:05:32.439][self$getEntryFields()$define] Define field description. biodb.DEBUG[2024-05-04 16:05:32.441][self$getEntryFields()$define] Define field name. biodb.DEBUG[2024-05-04 16:05:32.443][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2024-05-04 16:05:32.450][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-05-04 16:05:32.451][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2024-05-04 16:05:32.453][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2024-05-04 16:05:32.454][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2024-05-04 16:05:32.456][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2024-05-04 16:05:32.457][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2024-05-04 16:05:32.459][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-05-04 16:05:32.461][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2024-05-04 16:05:32.462][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2024-05-04 16:05:32.464][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2024-05-04 16:05:32.465][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2024-05-04 16:05:32.467][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-04 16:05:32.468][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2024-05-04 16:05:32.470][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2024-05-04 16:05:32.472][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-05-04 16:05:32.473][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2024-05-04 16:05:32.475][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2024-05-04 16:05:32.476][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2024-05-04 16:05:32.478][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2024-05-04 16:05:32.479][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2024-05-04 16:05:32.481][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2024-05-04 16:05:32.483][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2024-05-04 16:05:32.484][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2024-05-04 16:05:32.486][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2024-05-04 16:05:32.487][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2024-05-04 16:05:32.489][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2024-05-04 16:05:32.491][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2024-05-04 16:05:32.492][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2024-05-04 16:05:32.494][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2024-05-04 16:05:32.495][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2024-05-04 16:05:32.497][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2024-05-04 16:05:32.498][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2024-05-04 16:05:32.500][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2024-05-04 16:05:32.501][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2024-05-04 16:05:32.503][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2024-05-04 16:05:32.505][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2024-05-04 16:05:32.506][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2024-05-04 16:05:32.508][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2024-05-04 16:05:32.509][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2024-05-04 16:05:32.511][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2024-05-04 16:05:32.512][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2024-05-04 16:05:32.514][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2024-05-04 16:05:32.516][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2024-05-04 16:05:32.517][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2024-05-04 16:05:32.519][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2024-05-04 16:05:32.520][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2024-05-04 16:05:32.522][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2024-05-04 16:05:32.523][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2024-05-04 16:05:32.525][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2024-05-04 16:05:32.526][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2024-05-04 16:05:32.528][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2024-05-04 16:05:32.530][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2024-05-04 16:05:32.531][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2024-05-04 16:05:32.533][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2024-05-04 16:05:32.534][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2024-05-04 16:05:32.536][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2024-05-04 16:05:32.537][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2024-05-04 16:05:32.539][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2024-05-04 16:05:32.541][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2024-05-04 16:05:32.542][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2024-05-04 16:05:32.544][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2024-05-04 16:05:32.545][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2024-05-04 16:05:32.547][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-05-04 16:05:32.548][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-05-04 16:05:32.550][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2024-05-04 16:05:32.552][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2024-05-04 16:05:32.553][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2024-05-04 16:05:32.555][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2024-05-04 16:05:32.556][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2024-05-04 16:05:32.558][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2024-05-04 16:05:32.559][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2024-05-04 16:05:32.561][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2024-05-04 16:05:32.562][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2024-05-04 16:05:32.564][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2024-05-04 16:05:32.566][self$getEntryFields()$define] Define field products. biodb.DEBUG[2024-05-04 16:05:32.567][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2024-05-04 16:05:32.569][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2024-05-04 16:05:32.570][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2024-05-04 16:05:32.572][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2024-05-04 16:05:32.615][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2024-05-04 16:05:32.617][initialize] This is biodb version 1.12.0. biodb.DEBUG[2024-05-04 16:05:32.620][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 16:05:32.622][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:05:32.624][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:32.629][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:32.632][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:32.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:05:32.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:32.637][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:32.639][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:32.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.641][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 16:05:32.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.644][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:32.645][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:32.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:32.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.649][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 16:05:32.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.651][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:32.653][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:32.655][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:32.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.657][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 16:05:32.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.659][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:32.660][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:32.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:32.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:05:32.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.667][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 16:05:32.668][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:32.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:32.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.672][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 16:05:32.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.674][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:32.676][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:32.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:32.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:05:32.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.688][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 16:05:32.689][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:32.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:32.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:05:32.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:32.696][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:32.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:32.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.701][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 16:05:32.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.703][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:32.704][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:32.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:32.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.709][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 16:05:32.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:32.712][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:32.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:32.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.716][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 16:05:32.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.718][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:32.720][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:32.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:32.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.724][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 16:05:32.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.726][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:32.727][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:32.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:32.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.732][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 16:05:32.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.734][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:32.735][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:32.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:32.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.739][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 16:05:32.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.742][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 16:05:32.743][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:32.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:32.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.747][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 16:05:32.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:32.750][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:32.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:32.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.755][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 16:05:32.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:32.758][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:32.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:32.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:32.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.764][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 16:05:32.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.766][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:32.770][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml". biodb.DEBUG[2024-05-04 16:05:32.779][self$getDbsInfo()$define] Define connector expasy.enzyme. biodb.DEBUG[2024-05-04 16:05:32.781][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 16:05:32.782][self$setPropertyValue] Setting property "description" to "Write here the description of this database.". biodb.DEBUG[2024-05-04 16:05:32.783][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:05:32.784][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:05:32.786][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:05:32.787][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:05:32.788][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2024-05-04 16:05:32.789][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:05:32.790][self$setPropertyValue] Setting property "entry.content.type" to "txt". biodb.DEBUG[2024-05-04 16:05:32.792][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:05:32.793][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 16:05:32.794][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.". biodb.DEBUG[2024-05-04 16:05:32.795][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:05:32.797][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$". biodb.DEBUG[2024-05-04 16:05:32.797][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$". biodb.DEBUG[2024-05-04 16:05:32.797][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$". biodb.DEBUG[2024-05-04 16:05:32.797][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$". biodb.DEBUG[2024-05-04 16:05:32.798][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2024-05-04 16:05:32.799][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 16:05:32.800][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2024-05-04 16:05:32.801][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:05:32.802][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:05:32.804][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:05:32.805][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:05:32.806][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:05:32.807][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:05:32.808][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/". biodb.DEBUG[2024-05-04 16:05:32.810][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:05:32.811][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:05:32.812][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2024-05-04 16:05:32.813][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:05:32.819][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2024-05-04 16:05:32.840][super$initialize] Initialize connector expasy.enzyme. biodb.DEBUG[2024-05-04 16:05:32.842][super$initialize] Register connector expasy.enzyme with the request scheduler biodb.DEBUG[2024-05-04 16:05:32.845][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme. biodb.DEBUG[2024-05-04 16:05:32.849][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme". biodb.DEBUG[2024-05-04 16:05:32.853][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-04 16:05:32.854][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-04 16:05:32.855][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme . biodb.INFO [2024-05-04 16:05:32.865][biodb::testThat] biodb.INFO [2024-05-04 16:05:32.866][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value "). biodb.INFO [2024-05-04 16:05:32.868][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:05:32.869][biodb::testThat] biodb.TRACE[2024-05-04 16:05:32.876][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.1-content.txt". biodb.DEBUG[2024-05-04 16:05:32.878][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s). biodb.DEBUG[2024-05-04 16:05:32.881][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries. biodb.DEBUG[2024-05-04 16:05:32.901][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 16:05:32.902][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:32.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:32.957][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:32.958][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 16:05:32.959][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:32.960][FUN] Functions in observer BiodbConfig: [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 16:05:32.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:32.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:32.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:32.973][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:32.998][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity. biodb.TRACE[2024-05-04 16:05:33.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity. biodb.TRACE[2024-05-04 16:05:33.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.012][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.013][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor. biodb.TRACE[2024-05-04 16:05:33.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor. biodb.TRACE[2024-05-04 16:05:33.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.017][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.019][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:33.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:33.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.022][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.024][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR. biodb.TRACE[2024-05-04 16:05:33.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor. biodb.TRACE[2024-05-04 16:05:33.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.028][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.029][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor. biodb.TRACE[2024-05-04 16:05:33.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor. biodb.TRACE[2024-05-04 16:05:33.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.032][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.034][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor. biodb.TRACE[2024-05-04 16:05:33.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor. biodb.TRACE[2024-05-04 16:05:33.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.037][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.039][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor. biodb.TRACE[2024-05-04 16:05:33.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor. biodb.TRACE[2024-05-04 16:05:33.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.042][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.044][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR. biodb.TRACE[2024-05-04 16:05:33.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor. biodb.TRACE[2024-05-04 16:05:33.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.048][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.063][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:33.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:33.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.068][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.069][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:33.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:33.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.072][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.139][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:33.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:33.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.143][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.145][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:33.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:33.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.148][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.150][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:33.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:33.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.154][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.155][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:33.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:33.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.159][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.160][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:33.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:33.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.164][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.170][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.172][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:33.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:33.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.175][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.180][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.186][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.187][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.190][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.196][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.201][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.206][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 16:05:33.207][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1. biodb.TRACE[2024-05-04 16:05:33.210][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:05:33.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:05:33.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.214][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.215][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:05:33.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:05:33.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.221][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.222][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-04 16:05:33.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-04 16:05:33.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.226][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.227][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-04 16:05:33.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-04 16:05:33.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.231][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.272][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:33.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:33.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.275][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.287][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.292][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.297][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.309][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.314][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.319][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.320][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:33.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:33.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.324][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.325][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:33.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:33.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.329][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.330][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:33.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:33.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.334][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.350][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.355][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.360][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.362][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.363][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.364][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.365][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.370][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.382][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:33.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:33.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.385][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.387][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:33.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:33.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.390][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.392][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:33.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:33.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.395][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.397][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:33.398][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:33.399][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.400][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.401][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:33.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:33.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.416][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor. biodb.TRACE[2024-05-04 16:05:33.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor. biodb.TRACE[2024-05-04 16:05:33.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.420][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.421][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor. biodb.TRACE[2024-05-04 16:05:33.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor. biodb.TRACE[2024-05-04 16:05:33.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.425][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.426][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor. biodb.TRACE[2024-05-04 16:05:33.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor. biodb.TRACE[2024-05-04 16:05:33.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.429][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.431][ef$get] Asked field names are: cofactor. biodb.TRACE[2024-05-04 16:05:33.432][ef$get] Realnames of fields are: cofactor. biodb.TRACE[2024-05-04 16:05:33.433][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.434][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.436][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor. biodb.TRACE[2024-05-04 16:05:33.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor. biodb.TRACE[2024-05-04 16:05:33.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.439][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.450][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity. biodb.TRACE[2024-05-04 16:05:33.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity. biodb.TRACE[2024-05-04 16:05:33.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.454][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.455][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity. biodb.TRACE[2024-05-04 16:05:33.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity. biodb.TRACE[2024-05-04 16:05:33.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.459][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.460][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity. biodb.TRACE[2024-05-04 16:05:33.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity. biodb.TRACE[2024-05-04 16:05:33.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.464][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.465][ef$get] Asked field names are: catalytic.activity. biodb.TRACE[2024-05-04 16:05:33.467][ef$get] Realnames of fields are: catalytic.activity. biodb.TRACE[2024-05-04 16:05:33.468][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.469][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.470][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity. biodb.TRACE[2024-05-04 16:05:33.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity. biodb.TRACE[2024-05-04 16:05:33.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.474][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.486][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.487][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.489][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.490][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.502][ef$get] Asked field names are: catalytic.activity. biodb.TRACE[2024-05-04 16:05:33.504][ef$get] Realnames of fields are: catalytic.activity. biodb.TRACE[2024-05-04 16:05:33.505][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.506][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.513][ef$get] Asked field names are: cofactor. biodb.TRACE[2024-05-04 16:05:33.514][ef$get] Realnames of fields are: cofactor. biodb.TRACE[2024-05-04 16:05:33.516][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.517][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.528][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:33.529][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:33.531][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.532][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.553][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/testref/entry-expasy.enzyme-1.1.1.54-content.txt". biodb.DEBUG[2024-05-04 16:05:33.584][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s). biodb.DEBUG[2024-05-04 16:05:33.586][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries. biodb.DEBUG[2024-05-04 16:05:33.588][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 16:05:33.589][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:33.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:33.598][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:33.599][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 16:05:33.600][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:33.601][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.TRACE[2024-05-04 16:05:33.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.607][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.609][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity. biodb.TRACE[2024-05-04 16:05:33.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity. biodb.TRACE[2024-05-04 16:05:33.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.612][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.614][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:33.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:33.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.618][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.619][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR. biodb.TRACE[2024-05-04 16:05:33.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor. biodb.TRACE[2024-05-04 16:05:33.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.622][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.624][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:33.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:33.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.628][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.629][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:33.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:33.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.632][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.637][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.639][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:33.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:33.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.642][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.647][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.652][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.662][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.667][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.672][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.677][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 16:05:33.679][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54. biodb.TRACE[2024-05-04 16:05:33.698][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:05:33.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:05:33.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.702][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.703][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:05:33.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:05:33.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.707][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.708][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-04 16:05:33.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-04 16:05:33.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.712][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.713][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-04 16:05:33.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-04 16:05:33.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.717][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.723][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.730][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:33.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:33.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.734][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.744][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.749][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.754][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.762][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.768][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.772][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.774][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:33.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:33.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.778][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.779][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:33.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:33.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.783][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.784][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:33.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:33.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.787][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.812][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.817][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.823][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.829][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.830][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.831][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.836][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.848][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:33.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:33.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.852][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.853][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:33.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:33.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.856][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.858][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:33.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:33.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.861][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.863][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:33.864][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:33.865][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.866][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.867][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:33.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:33.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.871][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.883][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity. biodb.TRACE[2024-05-04 16:05:33.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity. biodb.TRACE[2024-05-04 16:05:33.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.887][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.888][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity. biodb.TRACE[2024-05-04 16:05:33.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity. biodb.TRACE[2024-05-04 16:05:33.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.892][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.893][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity. biodb.TRACE[2024-05-04 16:05:33.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity. biodb.TRACE[2024-05-04 16:05:33.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.897][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.898][ef$get] Asked field names are: catalytic.activity. biodb.TRACE[2024-05-04 16:05:33.899][ef$get] Realnames of fields are: catalytic.activity. biodb.TRACE[2024-05-04 16:05:33.901][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.902][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.903][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity. biodb.TRACE[2024-05-04 16:05:33.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity. biodb.TRACE[2024-05-04 16:05:33.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.907][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.919][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:33.921][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:33.922][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.923][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.930][ef$get] Asked field names are: catalytic.activity. biodb.TRACE[2024-05-04 16:05:33.932][ef$get] Realnames of fields are: catalytic.activity. biodb.TRACE[2024-05-04 16:05:33.933][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.934][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:33.941][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:33.942][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:33.943][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:33.945][ef$get] fields variable is a list. biodb.INFO [2024-05-04 16:05:33.962][biodb::testThat] biodb.INFO [2024-05-04 16:05:33.964][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. "). biodb.INFO [2024-05-04 16:05:33.966][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:05:33.967][biodb::testThat] biodb.DEBUG[2024-05-04 16:05:33.970][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54". biodb.DEBUG[2024-05-04 16:05:33.976][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)... biodb.TRACE[2024-05-04 16:05:33.995][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54". biodb.INFO [2024-05-04 16:05:33.997][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280". biodb.TRACE[2024-05-04 16:05:33.999][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE". biodb.TRACE[2024-05-04 16:05:34.001][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-04 16:05:34.002][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 16:05:34.004][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/". biodb.DEBUG[2024-05-04 16:05:34.005][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-05-04 16:05:34.006][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-05-04 16:05:34.011][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 16:05:34.012][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:34.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:34.021][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:34.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:05:34.023][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:34.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:34.025][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt". biodb.DEBUG[2024-05-04 16:05:34.050][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 16:05:34.051][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 16:05:34.052][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt". biodb.TRACE[2024-05-04 16:05:34.667][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/EC/1.1.1.1.txt does not exist. biodb.TRACE[2024-05-04 16:05:34.668][getUrlRequestResult] Using base::url() for sending request. biodb.DEBUG[2024-05-04 16:05:34.669][getUrlRequestResult] URL "https://enzyme.expasy.org/EC/1.1.1.1.txt" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url(). biodb.TRACE[2024-05-04 16:05:34.671][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt). biodb.DEBUG[2024-05-04 16:05:35.281][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-04 16:05:35.294][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content" biodb.TRACE[2024-05-04 16:05:35.309][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request" biodb.DEBUG[2024-05-04 16:05:35.312][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 16:05:35.313][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:35.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:35.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:35.323][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 16:05:35.325][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:35.326][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:35.345][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt". biodb.DEBUG[2024-05-04 16:05:35.359][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 16:05:35.361][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 16:05:35.374][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt". biodb.TRACE[2024-05-04 16:05:35.582][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/EC/1.1.1.54.txt does not exist. biodb.TRACE[2024-05-04 16:05:35.583][getUrlRequestResult] Using base::url() for sending request. biodb.DEBUG[2024-05-04 16:05:35.585][getUrlRequestResult] URL "https://enzyme.expasy.org/EC/1.1.1.54.txt" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url(). biodb.TRACE[2024-05-04 16:05:35.586][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt). biodb.DEBUG[2024-05-04 16:05:36.185][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-04 16:05:36.188][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content" biodb.TRACE[2024-05-04 16:05:36.198][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request" biodb.TRACE[2024-05-04 16:05:36.202][private$doSaveContentToFile] Saving to cache [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt" biodb.DEBUG[2024-05-04 16:05:36.205][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-05-04 16:05:36.207][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s). biodb.DEBUG[2024-05-04 16:05:36.208][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries. biodb.DEBUG[2024-05-04 16:05:36.210][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 16:05:36.211][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:36.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:36.219][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:36.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:05:36.222][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:36.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 16:05:36.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:36.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:36.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.229][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.231][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity. biodb.TRACE[2024-05-04 16:05:36.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity. biodb.TRACE[2024-05-04 16:05:36.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.234][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.236][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:36.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:36.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.240][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.241][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR. biodb.TRACE[2024-05-04 16:05:36.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor. biodb.TRACE[2024-05-04 16:05:36.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.245][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.246][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:36.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:36.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.250][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.251][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:36.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:36.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.255][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.256][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:36.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:36.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.260][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.261][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:36.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:36.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.265][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.266][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:36.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:36.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.270][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.271][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:36.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:36.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.275][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.276][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:36.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:36.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.280][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:36.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:36.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.285][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.286][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:36.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:36.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.289][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:36.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:36.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.295][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:36.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:36.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.300][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:36.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:36.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.304][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 16:05:36.306][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 16:05:36.308][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:36.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:36.318][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:36.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:05:36.320][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:36.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 16:05:36.324][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:36.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:36.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.328][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.330][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity. biodb.TRACE[2024-05-04 16:05:36.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity. biodb.TRACE[2024-05-04 16:05:36.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.333][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.335][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:36.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:36.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.339][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.340][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR. biodb.TRACE[2024-05-04 16:05:36.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor. biodb.TRACE[2024-05-04 16:05:36.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.348][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.350][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:36.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:36.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.353][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.355][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:36.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:36.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.358][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:36.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:36.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.363][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.364][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:36.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:05:36.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.368][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.369][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:36.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:36.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.373][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:36.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:36.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.378][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:36.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:36.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.383][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:36.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:36.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.388][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:36.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:36.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.393][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.394][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:36.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:36.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.398][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:36.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:36.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.403][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:36.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:36.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.408][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:05:36.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:05:36.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.413][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 16:05:36.414][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54. biodb.TRACE[2024-05-04 16:05:36.415][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt. biodb.TRACE[2024-05-04 16:05:36.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt. biodb.TRACE[2024-05-04 16:05:36.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.419][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.420][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min. biodb.TRACE[2024-05-04 16:05:36.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min. biodb.TRACE[2024-05-04 16:05:36.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.424][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.425][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max. biodb.TRACE[2024-05-04 16:05:36.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max. biodb.TRACE[2024-05-04 16:05:36.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.429][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.436][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt. biodb.TRACE[2024-05-04 16:05:36.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt. biodb.TRACE[2024-05-04 16:05:36.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.440][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.441][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min. biodb.TRACE[2024-05-04 16:05:36.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min. biodb.TRACE[2024-05-04 16:05:36.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.444][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.446][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max. biodb.TRACE[2024-05-04 16:05:36.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max. biodb.TRACE[2024-05-04 16:05:36.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.449][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-05-04 16:05:36.462][biodb::testThat] biodb.INFO [2024-05-04 16:05:36.463][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field "). biodb.INFO [2024-05-04 16:05:36.464][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:05:36.466][biodb::testThat] biodb.TRACE[2024-05-04 16:05:36.469][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:36.470][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:36.472][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.473][ef$get] fields variable is a list. biodb.DEBUG[2024-05-04 16:05:36.475][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name". biodb.TRACE[2024-05-04 16:05:36.509][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:36.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:36.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.513][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.514][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:36.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:36.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.518][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:36.519][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:36.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:36.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:36.523][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 16:05:36.527][function(conn, opt)] With value "alcohol dehydrogenase". biodb.DEBUG[2024-05-04 16:05:36.530][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase". biodb.DEBUG[2024-05-04 16:05:36.533][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 16:05:36.534][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 16:05:36.536][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase". biodb.TRACE[2024-05-04 16:05:36.744][doesRCurlRequestUrlExist] According to RCurl, URL https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase does not exist. biodb.TRACE[2024-05-04 16:05:36.746][getUrlRequestResult] Using base::url() for sending request. biodb.DEBUG[2024-05-04 16:05:36.747][getUrlRequestResult] URL "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url(). biodb.TRACE[2024-05-04 16:05:36.749][getBaseUrlRequestResult] Using base::url() for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase). biodb.DEBUG[2024-05-04 16:05:37.454][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-05-04 16:05:37.457][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content" biodb.TRACE[2024-05-04 16:05:37.462][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request" biodb.DEBUG[2024-05-04 16:05:37.468][function(conn, opt)] With found IDs [1]: "1.1.1.1". biodb.INFO [2024-05-04 16:05:37.491][biodb::testThat] biodb.INFO [2024-05-04 16:05:37.493][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. "). biodb.INFO [2024-05-04 16:05:37.494][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:05:37.495][biodb::testThat] biodb.TRACE[2024-05-04 16:05:37.522][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:37.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:37.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:37.526][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:37.527][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:37.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:37.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:37.537][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:37.538][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:37.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:37.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:37.542][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 16:05:37.570][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase". biodb.DEBUG[2024-05-04 16:05:37.573][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 16:05:37.587][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5". biodb.TRACE[2024-05-04 16:05:37.589][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 16:05:37.594][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content". biodb.INFO [2024-05-04 16:05:37.619][biodb::testThat] biodb.INFO [2024-05-04 16:05:37.621][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. "). biodb.INFO [2024-05-04 16:05:37.622][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:05:37.623][biodb::testThat] biodb.TRACE[2024-05-04 16:05:37.636][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:05:37.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:05:37.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:37.640][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:37.641][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:05:37.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:05:37.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:37.645][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:37.646][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-04 16:05:37.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-04 16:05:37.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:37.649][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:37.651][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-04 16:05:37.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-04 16:05:37.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:37.654][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:37.690][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:05:37.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:05:37.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:37.694][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:37.695][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:05:37.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:05:37.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:37.699][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:37.700][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-04 16:05:37.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-04 16:05:37.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:37.704][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:37.705][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-04 16:05:37.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-04 16:05:37.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:37.709][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-05-04 16:05:37.718][biodb::testThat] biodb.INFO [2024-05-04 16:05:37.719][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. "). biodb.INFO [2024-05-04 16:05:37.720][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:05:37.722][biodb::testThat] biodb.INFO [2024-05-04 16:05:37.734][biodb::testThat] biodb.INFO [2024-05-04 16:05:37.735][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. "). biodb.INFO [2024-05-04 16:05:37.736][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:05:37.738][biodb::testThat] biodb.INFO [2024-05-04 16:05:37.749][biodb::testThat] biodb.INFO [2024-05-04 16:05:37.750][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. "). biodb.INFO [2024-05-04 16:05:37.751][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:05:37.752][biodb::testThat] biodb.DEBUG[2024-05-04 16:05:37.767][function(conn, opt)] Trying to download "https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1". biodb.DEBUG[2024-05-04 16:05:37.985][getUrlContent] Use base::url() for downloading content of URL https://enzyme.expasy.org/cgi-bin/enzyme/enzyme-search-ec?field1=1&field2=1&field3=1&field4=1. biodb.INFO [2024-05-04 16:05:38.667][biodb::testThat] biodb.INFO [2024-05-04 16:05:38.669][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. "). biodb.INFO [2024-05-04 16:05:38.670][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:05:38.671][biodb::testThat] biodb.DEBUG[2024-05-04 16:05:38.883][getUrlContent] Use base::url() for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png. biodb.TRACE[2024-05-04 16:05:40.627][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:40.629][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:40.630][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:40.631][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:05:40.632][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:05:40.634][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:05:40.635][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:05:40.636][ef$get] fields variable is a list. biodb.INFO [2024-05-04 16:05:40.637][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2024-05-04 16:05:40.639][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler biodb.INFO [2024-05-04 16:05:40.640][self$deleteConn] Connector "expasy.enzyme" deleted. biodb.DEBUG[2024-05-04 16:05:40.641][notifyObservers] Notify observers for terminate. biodb.DEBUG[2024-05-04 16:05:40.642][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:40.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:40.645][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:40.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:05:40.647][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:40.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.INFO [2024-05-04 16:05:40.659][biodb::testContext] biodb.INFO [2024-05-04 16:05:40.660][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 16:05:40.661][biodb::testContext] Test context - Example long tests biodb.INFO [2024-05-04 16:05:40.663][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 16:05:40.664][biodb::testContext] biodb.INFO [2024-05-04 16:05:40.667][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0. biodb.DEBUG[2024-05-04 16:05:40.669][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc/R/library/biodb/definitions.yml". biodb.DEBUG[2024-05-04 16:05:40.674][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 16:05:40.676][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2024-05-04 16:05:40.677][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2024-05-04 16:05:40.678][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:40.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:40.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:40.682][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2024-05-04 16:05:40.683][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2024-05-04 16:05:40.684][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:40.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:40.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:40.688][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2024-05-04 16:05:40.689][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2024-05-04 16:05:40.690][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:40.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:40.692][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 16:05:40.693][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2024-05-04 16:05:40.695][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2024-05-04 16:05:40.696][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2024-05-04 16:05:40.697][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:40.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:40.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:40.700][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2024-05-04 16:05:40.702][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2024-05-04 16:05:40.704][self$set] Set key cache.system to TRUE. biodb.DEBUG[2024-05-04 16:05:40.705][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:40.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:40.708][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:40.709][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2024-05-04 16:05:40.710][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2024-05-04 16:05:40.711][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:40.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:40.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:40.715][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2024-05-04 16:05:40.716][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2024-05-04 16:05:40.717][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2024-05-04 16:05:40.719][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:40.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:40.721][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 16:05:40.722][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2024-05-04 16:05:40.723][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2024-05-04 16:05:40.724][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:40.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:40.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:40.728][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2024-05-04 16:05:40.729][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2024-05-04 16:05:40.730][self$set] Set key force.locale to TRUE. biodb.DEBUG[2024-05-04 16:05:40.737][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:40.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:40.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:40.740][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2024-05-04 16:05:40.742][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2024-05-04 16:05:40.743][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2024-05-04 16:05:40.744][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2024-05-04 16:05:40.745][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2024-05-04 16:05:40.746][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2024-05-04 16:05:40.748][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:40.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:40.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:40.751][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2024-05-04 16:05:40.752][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2024-05-04 16:05:40.753][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:40.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:40.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:40.757][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2024-05-04 16:05:40.758][self$set] Set key entries.sep to "|". biodb.DEBUG[2024-05-04 16:05:40.759][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:40.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:40.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:40.762][self$getConfig()$define] Define config key offline. biodb.DEBUG[2024-05-04 16:05:40.764][self$set] Set key offline to FALSE. biodb.DEBUG[2024-05-04 16:05:40.765][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:40.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:40.769][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 16:05:40.770][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2024-05-04 16:05:40.772][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2024-05-04 16:05:40.774][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:40.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:40.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:40.777][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2024-05-04 16:05:40.778][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2024-05-04 16:05:40.780][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:40.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:40.782][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:40.783][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2024-05-04 16:05:40.784][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2024-05-04 16:05:40.788][self$set] Set key svn.binary.path to "". biodb.DEBUG[2024-05-04 16:05:40.789][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:40.790][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:40.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:40.793][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2024-05-04 16:05:40.794][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2024-05-04 16:05:40.795][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2024-05-04 16:05:40.796][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:40.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:40.798][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:40.800][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2024-05-04 16:05:40.802][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 16:05:40.803][self$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 16:05:40.804][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:05:40.805][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:05:40.807][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:05:40.808][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:05:40.809][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:05:40.810][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:05:40.811][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 16:05:40.813][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:05:40.814][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 16:05:40.815][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2024-05-04 16:05:40.816][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:05:40.817][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:05:40.819][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:05:40.820][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 16:05:40.820][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 16:05:40.820][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 16:05:40.820][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 16:05:40.820][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 16:05:40.821][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:05:40.822][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:05:40.823][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:05:40.825][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:05:40.826][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:05:40.827][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:05:40.828][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:05:40.829][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:05:40.830][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:05:40.831][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:05:40.833][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:05:40.834][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:05:40.835][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2024-05-04 16:05:40.837][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 16:05:40.838][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 16:05:40.840][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:05:40.841][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:05:40.842][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:05:40.843][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:05:40.844][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:05:40.845][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:05:40.847][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 16:05:40.848][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:05:40.849][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 16:05:40.850][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2024-05-04 16:05:40.852][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:05:40.853][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:05:40.854][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:05:40.855][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 16:05:40.855][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 16:05:40.855][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 16:05:40.855][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 16:05:40.855][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 16:05:40.856][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:05:40.858][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:05:40.859][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:05:40.860][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:05:40.861][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:05:40.862][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:05:40.868][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:05:40.870][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:05:40.871][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:05:40.872][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:05:40.873][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:05:40.874][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:05:40.876][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2024-05-04 16:05:40.877][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 16:05:40.879][self$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 16:05:40.880][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:05:40.881][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:05:40.882][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:05:40.884][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:05:40.885][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:05:40.886][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:05:40.887][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 16:05:40.888][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:05:40.890][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 16:05:40.891][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2024-05-04 16:05:40.892][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:05:40.893][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:05:40.894][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:05:40.896][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:05:40.897][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:05:40.898][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:05:40.899][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:05:40.900][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:05:40.902][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:05:40.903][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:05:40.904][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:05:40.905][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:05:40.906][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:05:40.907][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:05:40.908][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:05:40.910][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:05:40.911][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2024-05-04 16:05:40.913][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 16:05:40.914][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 16:05:40.915][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:05:40.917][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:05:40.918][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:05:40.919][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:05:40.920][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:05:40.922][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:05:40.923][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 16:05:40.924][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:05:40.925][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 16:05:40.926][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2024-05-04 16:05:40.928][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:05:40.929][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:05:40.930][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:05:40.931][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:05:40.932][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:05:40.934][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:05:40.935][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:05:40.936][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:05:40.937][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:05:40.938][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:05:40.939][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:05:40.941][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:05:40.942][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:05:40.943][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:05:40.944][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:05:40.945][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:05:40.947][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 16:05:40.948][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:40.949][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:40.950][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:40.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:40.952][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 16:05:40.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:40.954][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:40.956][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:40.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:40.958][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 16:05:40.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:40.960][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:40.961][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:40.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:40.963][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 16:05:40.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:40.965][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:40.966][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:40.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:40.969][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 16:05:40.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:40.971][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:40.972][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:40.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:40.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:05:40.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:40.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:40.977][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:40.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:40.980][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 16:05:40.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:40.982][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:40.983][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:40.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:40.985][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 16:05:40.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:40.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:40.988][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:40.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:40.996][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 16:05:40.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:40.998][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:40.999][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:41.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:41.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:05:41.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:41.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:41.004][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:41.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:41.006][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 16:05:41.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:41.009][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 16:05:41.010][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:41.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:41.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:05:41.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:41.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:41.015][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:41.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:41.017][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 16:05:41.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:41.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:41.021][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:41.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:41.023][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 16:05:41.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:41.025][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 16:05:41.026][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:41.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:41.028][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 16:05:41.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:41.031][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:41.032][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:41.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:41.034][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 16:05:41.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:41.036][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 16:05:41.037][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:41.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:41.039][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 16:05:41.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:41.041][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:41.043][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:41.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:41.045][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 16:05:41.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:41.049][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:41.050][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2024-05-04 16:05:41.051][self$getEntryFields()$define] Define field description. biodb.DEBUG[2024-05-04 16:05:41.053][self$getEntryFields()$define] Define field name. biodb.DEBUG[2024-05-04 16:05:41.055][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2024-05-04 16:05:41.056][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-05-04 16:05:41.058][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2024-05-04 16:05:41.060][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2024-05-04 16:05:41.061][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2024-05-04 16:05:41.063][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2024-05-04 16:05:41.065][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2024-05-04 16:05:41.066][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-05-04 16:05:41.068][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2024-05-04 16:05:41.069][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2024-05-04 16:05:41.071][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2024-05-04 16:05:41.072][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2024-05-04 16:05:41.074][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-04 16:05:41.076][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2024-05-04 16:05:41.077][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2024-05-04 16:05:41.079][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-05-04 16:05:41.080][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2024-05-04 16:05:41.082][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2024-05-04 16:05:41.083][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2024-05-04 16:05:41.085][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2024-05-04 16:05:41.087][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2024-05-04 16:05:41.088][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2024-05-04 16:05:41.090][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2024-05-04 16:05:41.091][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2024-05-04 16:05:41.093][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2024-05-04 16:05:41.094][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2024-05-04 16:05:41.096][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2024-05-04 16:05:41.098][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2024-05-04 16:05:41.099][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2024-05-04 16:05:41.101][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2024-05-04 16:05:41.102][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2024-05-04 16:05:41.104][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2024-05-04 16:05:41.105][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2024-05-04 16:05:41.107][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2024-05-04 16:05:41.108][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2024-05-04 16:05:41.110][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2024-05-04 16:05:41.117][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2024-05-04 16:05:41.119][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2024-05-04 16:05:41.120][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2024-05-04 16:05:41.122][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2024-05-04 16:05:41.123][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2024-05-04 16:05:41.125][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2024-05-04 16:05:41.127][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2024-05-04 16:05:41.128][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2024-05-04 16:05:41.130][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2024-05-04 16:05:41.131][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2024-05-04 16:05:41.133][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2024-05-04 16:05:41.134][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2024-05-04 16:05:41.136][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2024-05-04 16:05:41.138][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2024-05-04 16:05:41.139][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2024-05-04 16:05:41.141][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2024-05-04 16:05:41.142][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2024-05-04 16:05:41.144][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2024-05-04 16:05:41.146][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2024-05-04 16:05:41.147][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2024-05-04 16:05:41.149][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2024-05-04 16:05:41.150][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2024-05-04 16:05:41.152][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2024-05-04 16:05:41.153][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2024-05-04 16:05:41.155][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2024-05-04 16:05:41.157][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2024-05-04 16:05:41.158][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2024-05-04 16:05:41.160][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-05-04 16:05:41.162][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-05-04 16:05:41.163][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2024-05-04 16:05:41.165][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2024-05-04 16:05:41.166][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2024-05-04 16:05:41.168][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2024-05-04 16:05:41.169][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2024-05-04 16:05:41.171][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2024-05-04 16:05:41.173][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2024-05-04 16:05:41.174][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2024-05-04 16:05:41.176][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2024-05-04 16:05:41.177][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2024-05-04 16:05:41.179][self$getEntryFields()$define] Define field products. biodb.DEBUG[2024-05-04 16:05:41.181][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2024-05-04 16:05:41.182][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2024-05-04 16:05:41.184][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2024-05-04 16:05:41.185][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2024-05-04 16:05:41.191][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2024-05-04 16:05:41.193][initialize] This is biodb version 1.12.0. biodb.DEBUG[2024-05-04 16:05:41.194][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 16:05:41.195][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:41.197][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 16:05:41.198][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:41.199][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:41.200][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:41.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:41.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:41.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:41.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:05:41.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:41.206][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:41.208][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:41.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:41.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:41.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:41.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:05:41.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:41.214][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:41.215][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:41.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:41.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:41.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:41.220][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 16:05:41.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:41.222][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:41.223][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:41.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:41.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:41.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:41.227][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 16:05:41.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:41.235][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:41.236][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:41.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:41.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:41.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:41.240][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 16:05:41.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:41.243][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:41.244][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:41.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:41.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:41.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:41.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:05:41.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:41.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:41.251][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:41.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:41.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:41.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:41.256][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 16:05:41.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:41.258][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:41.259][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:41.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:41.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:41.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:41.263][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 16:05:41.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:41.266][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:41.267][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:41.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:41.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:41.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:41.271][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 16:05:41.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:41.273][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:41.274][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:41.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:41.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:41.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:41.279][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 16:05:41.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:41.281][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:41.282][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:41.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:41.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:41.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:41.286][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 16:05:41.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:41.289][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:41.290][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:41.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:41.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:41.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:41.294][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 16:05:41.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:41.296][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:41.297][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:41.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:41.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:41.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:41.302][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 16:05:41.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:41.304][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:41.305][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:41.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:41.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:41.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:41.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:05:41.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:41.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:41.313][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:41.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:41.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:41.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:41.317][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 16:05:41.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:41.319][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:41.320][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:41.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:41.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:41.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:41.325][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 16:05:41.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:41.327][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:05:41.328][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:05:41.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:41.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:41.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:41.332][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 16:05:41.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:41.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:05:41.338][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml". biodb.DEBUG[2024-05-04 16:05:41.340][self$getDbsInfo()$define] Define connector expasy.enzyme. biodb.DEBUG[2024-05-04 16:05:41.342][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 16:05:41.343][self$setPropertyValue] Setting property "description" to "Write here the description of this database.". biodb.DEBUG[2024-05-04 16:05:41.344][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:05:41.345][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:05:41.347][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:05:41.348][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:05:41.349][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2024-05-04 16:05:41.350][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:05:41.351][self$setPropertyValue] Setting property "entry.content.type" to "txt". biodb.DEBUG[2024-05-04 16:05:41.353][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:05:41.359][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 16:05:41.360][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.". biodb.DEBUG[2024-05-04 16:05:41.361][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:05:41.363][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$". biodb.DEBUG[2024-05-04 16:05:41.363][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$". biodb.DEBUG[2024-05-04 16:05:41.363][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$". biodb.DEBUG[2024-05-04 16:05:41.363][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$". biodb.DEBUG[2024-05-04 16:05:41.364][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2024-05-04 16:05:41.365][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 16:05:41.366][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2024-05-04 16:05:41.368][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:05:41.369][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:05:41.370][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:05:41.371][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:05:41.372][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:05:41.374][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:05:41.375][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/". biodb.DEBUG[2024-05-04 16:05:41.376][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:05:41.377][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:05:41.378][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2024-05-04 16:05:41.379][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:05:41.381][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2024-05-04 16:05:41.385][super$initialize] Initialize connector expasy.enzyme. biodb.DEBUG[2024-05-04 16:05:41.386][super$initialize] Register connector expasy.enzyme with the request scheduler biodb.DEBUG[2024-05-04 16:05:41.387][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme. biodb.DEBUG[2024-05-04 16:05:41.389][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme". biodb.DEBUG[2024-05-04 16:05:41.391][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-04 16:05:41.392][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-04 16:05:41.393][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme . biodb.INFO [2024-05-04 16:05:41.394][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2024-05-04 16:05:41.396][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler biodb.INFO [2024-05-04 16:05:41.397][self$deleteConn] Connector "expasy.enzyme" deleted. biodb.DEBUG[2024-05-04 16:05:41.398][notifyObservers] Notify observers for terminate. biodb.DEBUG[2024-05-04 16:05:41.400][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:05:41.401][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:05:41.402][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:05:41.403][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 16:05:41.404][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:05:41.405][FUN] Functions in observer 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 86 ] > > proc.time() user system elapsed 5.28 0.43 11.36
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck' * using R version 4.4.0 beta (2024-04-15 r86425 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using options '--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error' * checking for file 'biodbExpasy/DESCRIPTION' ... OK * this is package 'biodbExpasy' 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 whether package 'biodbExpasy' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... 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 files in 'vignettes' ... SKIPPED * checking examples ... SKIPPED * checking for unstated dependencies in 'longtests' ... OK * checking tests in 'longtests' ... Running 'testthat.R' OK * DONE Status: 1 NOTE See 'F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/00check.log' for details.
biodbExpasy.Rcheck/00install.out
* installing *source* package 'biodbExpasy' ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbExpasy)