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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.8.0.tar.gz |
StartedAt: 2024-05-04 16:00:52 -0400 (Sat, 04 May 2024) |
EndedAt: 2024-05-04 16:01:41 -0400 (Sat, 04 May 2024) |
EllapsedTime: 49.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: biodbExpasy.Rcheck |
Warnings: 0 |
biodbExpasy.Rcheck/tests/testthat.Rout
R version 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # Script needed to run testthat automatically from ‘R CMD check’. See > # testthat::test_dir documentation. > library(testthat) > library(biodbExpasy) > Sys.setenv(TESTTHAT_REPORTER="summary") > Sys.setenv(BIODB_LOG_DST="console") > test_check("biodbExpasy") biodb.INFO [2024-05-04 16:01:30.980][biodb::testContext] biodb.INFO [2024-05-04 16:01:30.983][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 16:01:30.984][biodb::testContext] Test context - Generic long tests biodb.INFO [2024-05-04 16:01:30.985][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 16:01:30.986][biodb::testContext] biodb.INFO [2024-05-04 16:01:30.993][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0. biodb.DEBUG[2024-05-04 16:01:30.994][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml". biodb.DEBUG[2024-05-04 16:01:31.001][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 16:01:31.002][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2024-05-04 16:01:31.003][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2024-05-04 16:01:31.004][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:31.006][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2024-05-04 16:01:31.023][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2024-05-04 16:01:31.024][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.026][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:31.027][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2024-05-04 16:01:31.028][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2024-05-04 16:01:31.029][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:31.031][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2024-05-04 16:01:31.032][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2024-05-04 16:01:31.033][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2024-05-04 16:01:31.034][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.036][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 16:01:31.036][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2024-05-04 16:01:31.037][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2024-05-04 16:01:31.049][self$set] Set key cache.system to TRUE. biodb.DEBUG[2024-05-04 16:01:31.049][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:31.052][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2024-05-04 16:01:31.052][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2024-05-04 16:01:31.053][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.055][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:31.055][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2024-05-04 16:01:31.056][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2024-05-04 16:01:31.057][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2024-05-04 16:01:31.058][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:31.060][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2024-05-04 16:01:31.061][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2024-05-04 16:01:31.061][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.063][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:31.064][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2024-05-04 16:01:31.064][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2024-05-04 16:01:31.065][self$set] Set key force.locale to TRUE. biodb.DEBUG[2024-05-04 16:01:31.066][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:31.068][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2024-05-04 16:01:31.069][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2024-05-04 16:01:31.070][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2024-05-04 16:01:31.071][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2024-05-04 16:01:31.071][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2024-05-04 16:01:31.072][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2024-05-04 16:01:31.073][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:31.075][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2024-05-04 16:01:31.076][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2024-05-04 16:01:31.077][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:31.079][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2024-05-04 16:01:31.080][self$set] Set key entries.sep to "|". biodb.DEBUG[2024-05-04 16:01:31.081][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.082][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:31.083][self$getConfig()$define] Define config key offline. biodb.DEBUG[2024-05-04 16:01:31.084][self$set] Set key offline to FALSE. biodb.DEBUG[2024-05-04 16:01:31.085][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:31.087][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2024-05-04 16:01:31.088][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2024-05-04 16:01:31.089][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.090][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 16:01:31.091][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2024-05-04 16:01:31.092][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2024-05-04 16:01:31.092][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:31.094][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2024-05-04 16:01:31.095][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2024-05-04 16:01:31.113][self$set] Set key svn.binary.path to "". biodb.DEBUG[2024-05-04 16:01:31.114][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.115][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:31.116][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2024-05-04 16:01:31.117][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2024-05-04 16:01:31.118][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2024-05-04 16:01:31.119][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:31.123][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2024-05-04 16:01:31.149][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 16:01:31.162][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2024-05-04 16:01:31.163][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:01:31.164][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:01:31.165][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:01:31.166][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:01:31.167][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:01:31.167][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:01:31.168][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 16:01:31.169][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:01:31.170][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 16:01:31.171][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2024-05-04 16:01:31.172][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:01:31.172][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:31.173][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:01:31.174][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 16:01:31.174][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 16:01:31.174][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 16:01:31.174][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 16:01:31.174][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 16:01:31.175][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:01:31.176][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:01:31.177][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:01:31.177][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:01:31.178][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:01:31.179][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:01:31.180][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:01:31.181][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:31.182][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:01:31.182][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:01:31.183][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:01:31.184][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:31.185][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2024-05-04 16:01:31.186][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 16:01:31.187][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 16:01:31.188][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:01:31.189][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:01:31.190][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:01:31.190][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:01:31.191][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:01:31.192][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:01:31.193][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 16:01:31.194][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:01:31.195][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 16:01:31.196][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2024-05-04 16:01:31.196][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:01:31.197][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:31.198][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:01:31.199][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 16:01:31.199][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 16:01:31.199][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 16:01:31.199][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 16:01:31.199][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 16:01:31.200][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:01:31.201][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:01:31.201][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:01:31.202][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:01:31.203][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:01:31.204][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:01:31.204][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:01:31.205][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:31.206][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:01:31.207][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:01:31.208][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:01:31.209][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:31.210][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2024-05-04 16:01:31.211][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 16:01:31.212][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2024-05-04 16:01:31.213][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:01:31.214][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:01:31.215][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:01:31.215][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:01:31.216][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:01:31.217][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:01:31.218][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 16:01:31.218][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:01:31.219][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 16:01:31.220][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2024-05-04 16:01:31.221][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:01:31.222][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:31.223][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:01:31.228][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:31.229][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:01:31.230][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:01:31.231][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:01:31.231][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:01:31.232][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:01:31.233][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:01:31.234][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:01:31.234][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:31.235][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:01:31.236][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:01:31.237][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:01:31.237][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:31.238][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2024-05-04 16:01:31.240][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 16:01:31.240][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 16:01:31.241][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:01:31.242][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:01:31.243][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:01:31.244][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:01:31.244][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:01:31.245][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:01:31.246][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 16:01:31.247][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:01:31.248][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 16:01:31.248][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2024-05-04 16:01:31.249][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:01:31.250][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:31.251][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:01:31.251][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:31.252][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:01:31.253][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:01:31.254][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:01:31.254][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:01:31.255][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:01:31.256][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:01:31.256][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:01:31.257][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:31.258][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:01:31.259][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:01:31.260][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:01:31.260][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:31.264][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 16:01:31.265][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.265][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:31.266][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.268][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 16:01:31.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.269][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:31.270][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.271][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 16:01:31.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.273][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 16:01:31.274][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.275][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 16:01:31.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.277][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:31.277][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.279][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 16:01:31.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.280][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:31.281][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.283][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 16:01:31.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.284][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:31.285][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.286][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 16:01:31.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:31.289][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.290][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 16:01:31.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.291][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:31.292][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.294][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 16:01:31.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.295][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:31.296][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.297][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 16:01:31.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.299][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:31.300][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.301][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 16:01:31.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.303][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:31.303][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.305][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 16:01:31.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.306][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:31.307][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.309][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 16:01:31.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:31.311][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.312][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 16:01:31.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:31.314][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.316][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 16:01:31.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.317][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:31.318][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.320][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 16:01:31.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.321][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:31.322][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.323][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 16:01:31.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:31.325][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.327][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 16:01:31.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.328][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:31.329][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2024-05-04 16:01:31.333][self$getEntryFields()$define] Define field description. biodb.DEBUG[2024-05-04 16:01:31.334][self$getEntryFields()$define] Define field name. biodb.DEBUG[2024-05-04 16:01:31.336][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2024-05-04 16:01:31.337][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-05-04 16:01:31.338][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2024-05-04 16:01:31.339][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2024-05-04 16:01:31.340][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2024-05-04 16:01:31.341][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2024-05-04 16:01:31.342][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2024-05-04 16:01:31.343][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-05-04 16:01:31.344][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2024-05-04 16:01:31.346][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2024-05-04 16:01:31.347][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2024-05-04 16:01:31.348][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2024-05-04 16:01:31.349][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-04 16:01:31.350][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2024-05-04 16:01:31.351][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2024-05-04 16:01:31.352][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-05-04 16:01:31.353][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2024-05-04 16:01:31.355][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2024-05-04 16:01:31.356][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2024-05-04 16:01:31.357][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2024-05-04 16:01:31.358][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2024-05-04 16:01:31.359][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2024-05-04 16:01:31.360][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2024-05-04 16:01:31.362][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2024-05-04 16:01:31.363][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2024-05-04 16:01:31.364][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2024-05-04 16:01:31.365][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2024-05-04 16:01:31.366][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2024-05-04 16:01:31.367][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2024-05-04 16:01:31.369][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2024-05-04 16:01:31.370][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2024-05-04 16:01:31.371][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2024-05-04 16:01:31.372][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2024-05-04 16:01:31.373][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2024-05-04 16:01:31.374][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2024-05-04 16:01:31.375][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2024-05-04 16:01:31.376][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2024-05-04 16:01:31.378][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2024-05-04 16:01:31.379][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2024-05-04 16:01:31.380][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2024-05-04 16:01:31.381][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2024-05-04 16:01:31.382][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2024-05-04 16:01:31.384][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2024-05-04 16:01:31.385][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2024-05-04 16:01:31.386][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2024-05-04 16:01:31.387][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2024-05-04 16:01:31.393][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2024-05-04 16:01:31.394][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2024-05-04 16:01:31.396][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2024-05-04 16:01:31.397][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2024-05-04 16:01:31.398][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2024-05-04 16:01:31.399][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2024-05-04 16:01:31.400][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2024-05-04 16:01:31.401][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2024-05-04 16:01:31.402][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2024-05-04 16:01:31.403][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2024-05-04 16:01:31.405][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2024-05-04 16:01:31.406][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2024-05-04 16:01:31.407][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2024-05-04 16:01:31.408][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2024-05-04 16:01:31.409][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2024-05-04 16:01:31.410][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2024-05-04 16:01:31.411][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2024-05-04 16:01:31.412][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-05-04 16:01:31.413][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-05-04 16:01:31.414][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2024-05-04 16:01:31.415][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2024-05-04 16:01:31.417][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2024-05-04 16:01:31.418][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2024-05-04 16:01:31.419][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2024-05-04 16:01:31.420][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2024-05-04 16:01:31.421][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2024-05-04 16:01:31.422][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2024-05-04 16:01:31.423][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2024-05-04 16:01:31.424][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2024-05-04 16:01:31.425][self$getEntryFields()$define] Define field products. biodb.DEBUG[2024-05-04 16:01:31.427][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2024-05-04 16:01:31.428][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2024-05-04 16:01:31.429][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2024-05-04 16:01:31.430][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2024-05-04 16:01:31.434][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2024-05-04 16:01:31.436][initialize] This is biodb version 1.12.0. biodb.DEBUG[2024-05-04 16:01:31.439][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 16:01:31.439][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.440][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 16:01:31.441][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.442][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:31.446][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:31.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:31.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.449][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 16:01:31.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.450][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:31.451][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:31.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:31.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.454][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 16:01:31.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:31.456][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:31.458][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:31.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.459][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 16:01:31.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.461][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:31.461][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:31.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:31.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.464][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 16:01:31.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.466][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:31.467][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:31.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:31.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.470][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 16:01:31.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:31.472][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:31.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:31.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.475][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 16:01:31.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:31.477][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:31.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:31.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.480][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 16:01:31.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.482][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:31.482][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:31.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:31.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.485][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 16:01:31.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.487][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:31.488][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:31.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:31.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:31.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:31.493][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:31.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:31.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.496][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 16:01:31.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:31.498][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:31.500][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:31.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:31.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:31.503][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:31.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:31.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.506][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 16:01:31.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.508][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:31.508][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:31.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:31.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:31.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:31.514][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:31.515][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:31.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.517][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 16:01:31.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:31.519][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:31.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:31.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.522][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 16:01:31.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.524][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:31.524][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:31.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:31.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.527][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 16:01:31.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:31.530][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:31.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:31.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:31.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.533][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 16:01:31.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.534][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:31.537][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml". biodb.DEBUG[2024-05-04 16:01:31.545][self$getDbsInfo()$define] Define connector expasy.enzyme. biodb.DEBUG[2024-05-04 16:01:31.547][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 16:01:31.548][self$setPropertyValue] Setting property "description" to "Write here the description of this database.". biodb.DEBUG[2024-05-04 16:01:31.549][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:01:31.549][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:01:31.554][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:01:31.555][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:01:31.556][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2024-05-04 16:01:31.557][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:01:31.558][self$setPropertyValue] Setting property "entry.content.type" to "txt". biodb.DEBUG[2024-05-04 16:01:31.559][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:01:31.559][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 16:01:31.560][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.". biodb.DEBUG[2024-05-04 16:01:31.561][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:01:31.562][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$". biodb.DEBUG[2024-05-04 16:01:31.562][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$". biodb.DEBUG[2024-05-04 16:01:31.562][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$". biodb.DEBUG[2024-05-04 16:01:31.562][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$". biodb.DEBUG[2024-05-04 16:01:31.563][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2024-05-04 16:01:31.564][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 16:01:31.564][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2024-05-04 16:01:31.565][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:01:31.566][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:01:31.567][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:01:31.568][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:01:31.568][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:01:31.569][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:01:31.570][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/". biodb.DEBUG[2024-05-04 16:01:31.571][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:01:31.572][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:01:31.572][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2024-05-04 16:01:31.573][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:31.578][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2024-05-04 16:01:31.600][super$initialize] Initialize connector expasy.enzyme. biodb.DEBUG[2024-05-04 16:01:31.601][super$initialize] Register connector expasy.enzyme with the request scheduler biodb.DEBUG[2024-05-04 16:01:31.605][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme. biodb.DEBUG[2024-05-04 16:01:31.608][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme". biodb.DEBUG[2024-05-04 16:01:31.612][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-04 16:01:31.613][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-04 16:01:31.613][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme . biodb.INFO [2024-05-04 16:01:31.622][biodb::testThat] biodb.INFO [2024-05-04 16:01:31.622][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value "). biodb.INFO [2024-05-04 16:01:31.623][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:01:31.624][biodb::testThat] biodb.TRACE[2024-05-04 16:01:31.627][loadFileContents] Loaded 1 files from cache: [1]: "/Users/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 16:01:31.628][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s). biodb.DEBUG[2024-05-04 16:01:31.631][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries. biodb.DEBUG[2024-05-04 16:01:31.638][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 16:01:31.639][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:31.639][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:31.651][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:31.652][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 16:01:31.653][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:31.653][FUN] Functions in observer BiodbConfig: [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 16:01:31.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:31.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:31.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.665][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.685][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity. biodb.TRACE[2024-05-04 16:01:31.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity. biodb.TRACE[2024-05-04 16:01:31.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.697][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.698][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor. biodb.TRACE[2024-05-04 16:01:31.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor. biodb.TRACE[2024-05-04 16:01:31.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.700][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.701][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:31.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:31.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.704][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.705][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR. biodb.TRACE[2024-05-04 16:01:31.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor. biodb.TRACE[2024-05-04 16:01:31.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.707][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.708][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor. biodb.TRACE[2024-05-04 16:01:31.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor. biodb.TRACE[2024-05-04 16:01:31.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.710][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.711][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor. biodb.TRACE[2024-05-04 16:01:31.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor. biodb.TRACE[2024-05-04 16:01:31.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.713][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.714][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor. biodb.TRACE[2024-05-04 16:01:31.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor. biodb.TRACE[2024-05-04 16:01:31.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.717][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.718][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR. biodb.TRACE[2024-05-04 16:01:31.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor. biodb.TRACE[2024-05-04 16:01:31.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.720][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.743][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:31.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:31.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.745][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.746][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:31.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:31.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.749][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.774][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:31.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:31.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.777][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.778][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:31.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:31.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.781][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.781][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:31.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:31.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.784][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.785][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:31.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:31.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.787][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.788][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:31.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:31.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.791][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:31.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:31.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.794][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.795][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:31.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:31.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.797][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:31.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:31.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.800][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:31.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:31.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.804][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:31.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:31.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.807][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:31.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:31.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.810][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:31.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:31.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.814][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:31.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:31.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.817][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 16:01:31.818][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.1. biodb.TRACE[2024-05-04 16:01:31.820][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:01:31.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:01:31.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.822][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.823][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:01:31.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:01:31.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.826][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.826][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-04 16:01:31.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-04 16:01:31.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.829][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.830][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-04 16:01:31.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-04 16:01:31.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.832][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:31.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:31.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.849][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.891][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:31.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:31.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.893][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:31.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:31.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.901][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:31.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:31.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.904][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:31.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:31.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.907][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:31.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:31.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.912][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:31.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:31.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.916][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:31.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:31.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.919][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.920][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:31.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:31.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.923][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.923][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:31.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:31.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.926][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.927][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:31.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:31.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.929][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:31.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:31.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.940][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:31.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:31.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.943][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:31.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:31.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.946][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.947][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:31.948][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:31.949][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.950][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:31.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:31.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.953][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.962][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:31.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:31.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.965][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:31.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:31.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.968][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.968][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:31.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:31.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.971][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.972][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:31.972][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:31.973][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.974][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.975][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:31.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:31.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.977][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.986][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor. biodb.TRACE[2024-05-04 16:01:31.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor. biodb.TRACE[2024-05-04 16:01:31.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.988][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.989][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor. biodb.TRACE[2024-05-04 16:01:31.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor. biodb.TRACE[2024-05-04 16:01:31.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.992][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.992][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor. biodb.TRACE[2024-05-04 16:01:31.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor. biodb.TRACE[2024-05-04 16:01:31.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.995][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.995][ef$get] Asked field names are: cofactor. biodb.TRACE[2024-05-04 16:01:31.996][ef$get] Realnames of fields are: cofactor. biodb.TRACE[2024-05-04 16:01:31.997][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:31.998][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:31.999][self$getBiodb()$getEntryFields()$get] Asked field names are: cofactor. biodb.TRACE[2024-05-04 16:01:31.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor. biodb.TRACE[2024-05-04 16:01:32.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.001][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.010][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity. biodb.TRACE[2024-05-04 16:01:32.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity. biodb.TRACE[2024-05-04 16:01:32.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.012][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.013][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity. biodb.TRACE[2024-05-04 16:01:32.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity. biodb.TRACE[2024-05-04 16:01:32.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.016][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.017][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity. biodb.TRACE[2024-05-04 16:01:32.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity. biodb.TRACE[2024-05-04 16:01:32.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.019][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.020][ef$get] Asked field names are: catalytic.activity. biodb.TRACE[2024-05-04 16:01:32.021][ef$get] Realnames of fields are: catalytic.activity. biodb.TRACE[2024-05-04 16:01:32.022][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.022][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.023][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity. biodb.TRACE[2024-05-04 16:01:32.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity. biodb.TRACE[2024-05-04 16:01:32.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.026][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.034][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:32.039][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:32.041][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.041][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.046][ef$get] Asked field names are: catalytic.activity. biodb.TRACE[2024-05-04 16:01:32.047][ef$get] Realnames of fields are: catalytic.activity. biodb.TRACE[2024-05-04 16:01:32.047][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.048][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.052][ef$get] Asked field names are: cofactor. biodb.TRACE[2024-05-04 16:01:32.053][ef$get] Realnames of fields are: cofactor. biodb.TRACE[2024-05-04 16:01:32.054][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.055][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.059][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:32.060][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:32.061][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.062][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.076][loadFileContents] Loaded 1 files from cache: [1]: "/Users/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 16:01:32.104][biodb$getFactory()$createEntryFromCo ...] Creating Expasy ENZYME database. entries from 1 content(s). biodb.DEBUG[2024-05-04 16:01:32.105][biodb$getFactory()$createEntryFromCo ...] Parsing 1 Expasy ENZYME database. entries. biodb.DEBUG[2024-05-04 16:01:32.107][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 16:01:32.108][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:32.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:32.113][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:32.114][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 16:01:32.114][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:32.115][FUN] Functions in observer BiodbConfig: [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 16:01:32.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:32.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:32.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.119][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.120][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity. biodb.TRACE[2024-05-04 16:01:32.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity. biodb.TRACE[2024-05-04 16:01:32.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.123][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.124][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:32.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:32.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.126][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.127][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR. biodb.TRACE[2024-05-04 16:01:32.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor. biodb.TRACE[2024-05-04 16:01:32.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.130][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.131][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:32.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:32.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.133][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.134][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:32.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:32.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.137][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:32.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:32.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.140][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.141][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:32.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:32.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.143][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:32.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:32.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.147][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:32.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:32.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.150][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:32.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:32.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.153][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:32.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:32.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.157][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:32.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:32.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.160][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:32.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:32.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.164][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 16:01:32.164][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 1.1.1.54. biodb.TRACE[2024-05-04 16:01:32.185][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:01:32.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:01:32.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.187][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.188][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:01:32.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:01:32.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.191][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.191][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-04 16:01:32.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-04 16:01:32.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.194][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.195][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-04 16:01:32.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-04 16:01:32.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.197][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:32.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:32.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.201][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.206][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:32.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:32.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.209][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.214][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:32.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:32.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.216][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:32.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:32.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.220][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:32.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:32.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.223][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:32.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:32.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.228][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:32.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:32.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.231][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:32.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:32.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.235][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.236][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:32.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:32.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.238][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.239][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:32.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:32.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.242][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.242][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:32.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:32.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.245][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:32.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:32.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.263][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:32.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:32.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.266][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:32.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:32.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.270][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.271][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:32.272][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:32.273][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.273][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:32.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:32.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.277][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.285][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:32.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:32.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.288][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.289][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:32.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:32.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.292][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.293][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:32.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:32.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.296][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.297][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:32.297][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:32.298][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.299][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.300][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:32.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:32.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.302][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.315][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity. biodb.TRACE[2024-05-04 16:01:32.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity. biodb.TRACE[2024-05-04 16:01:32.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.318][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.319][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity. biodb.TRACE[2024-05-04 16:01:32.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity. biodb.TRACE[2024-05-04 16:01:32.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.321][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.322][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity. biodb.TRACE[2024-05-04 16:01:32.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity. biodb.TRACE[2024-05-04 16:01:32.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.325][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.326][ef$get] Asked field names are: catalytic.activity. biodb.TRACE[2024-05-04 16:01:32.326][ef$get] Realnames of fields are: catalytic.activity. biodb.TRACE[2024-05-04 16:01:32.327][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.328][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.329][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity. biodb.TRACE[2024-05-04 16:01:32.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity. biodb.TRACE[2024-05-04 16:01:32.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.331][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.340][ef$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:32.341][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:32.342][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.342][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.347][ef$get] Asked field names are: catalytic.activity. biodb.TRACE[2024-05-04 16:01:32.348][ef$get] Realnames of fields are: catalytic.activity. biodb.TRACE[2024-05-04 16:01:32.349][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.350][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:32.354][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:32.355][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:32.356][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:32.357][ef$get] fields variable is a list. biodb.INFO [2024-05-04 16:01:32.365][biodb::testThat] biodb.INFO [2024-05-04 16:01:32.366][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. "). biodb.INFO [2024-05-04 16:01:32.367][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:01:32.367][biodb::testThat] biodb.DEBUG[2024-05-04 16:01:32.369][private$loadEntries] Creating entries from ids [2]: "1.1.1.1, 1.1.1.54". biodb.DEBUG[2024-05-04 16:01:32.375][conn$getEntryContent] Get Expasy ENZYME database. entry content(s) for 2 id(s)... biodb.TRACE[2024-05-04 16:01:32.380][cch$loadFileContent] Trying to load 2 files from cache: [2]: "1.1.1.1, 1.1.1.54". biodb.INFO [2024-05-04 16:01:32.381][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280" for "expasy.enzyme-b59b84d962b6741050ba8f70ff4db280". biodb.TRACE[2024-05-04 16:01:32.383][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE". biodb.TRACE[2024-05-04 16:01:32.384][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-05-04 16:01:32.385][conn$getEntryContent] 0 Expasy ENZYME database. entry content(s) loaded from cache. biodb.DEBUG[2024-05-04 16:01:32.385][conn$getEntryContent] 2 entry content(s) need to be fetched from Expasy ENZYME database. database "https://enzyme.expasy.org/". biodb.DEBUG[2024-05-04 16:01:32.386][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-05-04 16:01:32.387][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-05-04 16:01:32.392][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 16:01:32.393][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:32.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:32.398][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:32.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:32.400][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:32.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:32.402][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.1.txt". biodb.DEBUG[2024-05-04 16:01:32.419][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 16:01:32.420][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 16:01:32.421][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.1.txt". biodb.TRACE[2024-05-04 16:01:33.434][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.1.txt). biodb.DEBUG[2024-05-04 16:01:34.237][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-04 16:01:34.239][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.content" biodb.TRACE[2024-05-04 16:01:34.251][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a52675cfd2f0c2b41556caa64d9341e3.request" biodb.DEBUG[2024-05-04 16:01:34.253][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 16:01:34.254][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:34.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:34.259][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:34.260][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 16:01:34.260][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:34.261][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:34.277][scheduler$sendRequest] Getting content of get URL request "https://enzyme.expasy.org/EC/1.1.1.54.txt". biodb.DEBUG[2024-05-04 16:01:34.298][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 16:01:34.299][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 16:01:34.310][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/EC/1.1.1.54.txt". biodb.TRACE[2024-05-04 16:01:35.229][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/EC/1.1.1.54.txt). biodb.DEBUG[2024-05-04 16:01:35.971][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-05-04 16:01:35.973][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.content" biodb.TRACE[2024-05-04 16:01:35.976][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/a9b93566a091cbe35a06e4b3871f95c9.request" biodb.TRACE[2024-05-04 16:01:35.978][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.1.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/1.1.1.54.txt" biodb.DEBUG[2024-05-04 16:01:35.979][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-05-04 16:01:35.980][self$createEntryFromContent] Creating Expasy ENZYME database. entries from 2 content(s). biodb.DEBUG[2024-05-04 16:01:35.990][self$createEntryFromContent] Parsing 2 Expasy ENZYME database. entries. biodb.DEBUG[2024-05-04 16:01:35.992][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 16:01:35.992][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:35.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:36.020][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:36.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:36.049][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:36.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 16:01:36.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:36.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:36.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.096][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.098][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity. biodb.TRACE[2024-05-04 16:01:36.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity. biodb.TRACE[2024-05-04 16:01:36.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.100][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.101][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:36.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:36.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.104][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.122][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR. biodb.TRACE[2024-05-04 16:01:36.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor. biodb.TRACE[2024-05-04 16:01:36.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.144][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.145][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:36.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:36.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.148][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.149][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:36.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:36.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.151][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.152][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:36.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:36.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.155][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.155][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:36.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:36.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.158][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.159][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:36.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:36.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.161][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.162][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:36.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:36.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.165][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.166][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:36.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:36.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.168][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:36.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:36.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.172][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.173][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:36.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:36.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.175][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:36.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:36.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.178][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:36.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:36.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.182][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:36.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:36.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.189][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 16:01:36.193][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-05-04 16:01:36.194][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:36.195][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:36.199][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:36.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:36.201][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:36.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-05-04 16:01:36.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:36.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:36.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.206][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.207][self$getBiodb()$getEntryFields()$get] Asked field names are: catalytic.activity. biodb.TRACE[2024-05-04 16:01:36.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: catalytic.activity. biodb.TRACE[2024-05-04 16:01:36.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.209][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.210][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:36.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:36.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.213][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.214][self$getBiodb()$getEntryFields()$get] Asked field names are: COFACTOR. biodb.TRACE[2024-05-04 16:01:36.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cofactor. biodb.TRACE[2024-05-04 16:01:36.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.216][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.217][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:36.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:36.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.219][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.220][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:36.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:36.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.223][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:36.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:36.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.226][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.227][self$getBiodb()$getEntryFields()$get] Asked field names are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:36.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: expasy.enzyme.id. biodb.TRACE[2024-05-04 16:01:36.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.229][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:36.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:36.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.233][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:36.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:36.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.236][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:36.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:36.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.240][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:36.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:36.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.243][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:36.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:36.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.246][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:36.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:36.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.249][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:36.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:36.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.253][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:36.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:36.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.256][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-05-04 16:01:36.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-05-04 16:01:36.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.259][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 16:01:36.260][self$createEntryFromContent] Accession numbers: 1.1.1.1, 1.1.1.54. biodb.TRACE[2024-05-04 16:01:36.261][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt. biodb.TRACE[2024-05-04 16:01:36.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt. biodb.TRACE[2024-05-04 16:01:36.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.263][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.264][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min. biodb.TRACE[2024-05-04 16:01:36.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min. biodb.TRACE[2024-05-04 16:01:36.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.267][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.267][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max. biodb.TRACE[2024-05-04 16:01:36.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max. biodb.TRACE[2024-05-04 16:01:36.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.270][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.275][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt. biodb.TRACE[2024-05-04 16:01:36.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt. biodb.TRACE[2024-05-04 16:01:36.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.278][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.278][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min. biodb.TRACE[2024-05-04 16:01:36.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min. biodb.TRACE[2024-05-04 16:01:36.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.281][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.282][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max. biodb.TRACE[2024-05-04 16:01:36.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max. biodb.TRACE[2024-05-04 16:01:36.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.284][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-05-04 16:01:36.293][biodb::testThat] biodb.INFO [2024-05-04 16:01:36.293][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field "). biodb.INFO [2024-05-04 16:01:36.294][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:01:36.295][biodb::testThat] biodb.TRACE[2024-05-04 16:01:36.298][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:36.299][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:36.300][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.300][ef$get] fields variable is a list. biodb.DEBUG[2024-05-04 16:01:36.301][function(conn, opt)] Testing searchForEntries() with entry "1.1.1.1" and field "name". biodb.TRACE[2024-05-04 16:01:36.328][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:36.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:36.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.331][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.332][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:36.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:36.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.335][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:36.336][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:36.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:36.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:36.338][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 16:01:36.342][function(conn, opt)] With value "alcohol dehydrogenase". biodb.DEBUG[2024-05-04 16:01:36.344][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase". biodb.DEBUG[2024-05-04 16:01:36.346][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-05-04 16:01:36.347][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-05-04 16:01:36.348][private$doSendRequestOnce] Sent URL is "https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase". biodb.TRACE[2024-05-04 16:01:36.966][getRCurlRequestResult] Using RCurl package for sending request (https://enzyme.expasy.org/enzyme-byname.html?alcohol%20dehydrogenase). biodb.DEBUG[2024-05-04 16:01:37.632][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-05-04 16:01:37.634][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content" biodb.TRACE[2024-05-04 16:01:37.637][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.request" biodb.DEBUG[2024-05-04 16:01:37.642][function(conn, opt)] With found IDs [1]: "1.1.1.1". biodb.INFO [2024-05-04 16:01:37.657][biodb::testThat] biodb.INFO [2024-05-04 16:01:37.658][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. "). biodb.INFO [2024-05-04 16:01:37.659][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:01:37.660][biodb::testThat] biodb.TRACE[2024-05-04 16:01:37.681][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:37.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:37.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:37.683][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:37.684][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:37.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:37.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:37.687][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:37.688][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:37.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:37.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:37.690][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-05-04 16:01:37.720][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://enzyme.expasy.org/enzyme-byname.html?alcohol dehydrogenase". biodb.DEBUG[2024-05-04 16:01:37.722][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-05-04 16:01:37.734][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f603fa2a57aec59588edc37541c6f6d5". biodb.TRACE[2024-05-04 16:01:37.735][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-05-04 16:01:37.737][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/expasy.enzyme-b59b84d962b6741050ba8f70ff4db280/f603fa2a57aec59588edc37541c6f6d5.content". biodb.INFO [2024-05-04 16:01:37.754][biodb::testThat] biodb.INFO [2024-05-04 16:01:37.754][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. "). biodb.INFO [2024-05-04 16:01:37.755][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:01:37.756][biodb::testThat] biodb.TRACE[2024-05-04 16:01:37.765][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:01:37.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:01:37.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:37.768][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:37.769][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:01:37.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:01:37.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:37.771][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:37.772][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-04 16:01:37.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-04 16:01:37.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:37.775][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:37.775][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-04 16:01:37.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-04 16:01:37.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:37.778][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:37.809][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:01:37.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:01:37.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:37.812][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:37.813][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-05-04 16:01:37.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-05-04 16:01:37.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:37.815][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:37.816][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-05-04 16:01:37.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-05-04 16:01:37.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:37.819][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:37.820][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-05-04 16:01:37.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-05-04 16:01:37.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:37.822][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-05-04 16:01:37.828][biodb::testThat] biodb.INFO [2024-05-04 16:01:37.829][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. "). biodb.INFO [2024-05-04 16:01:37.830][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:01:37.831][biodb::testThat] biodb.INFO [2024-05-04 16:01:37.839][biodb::testThat] biodb.INFO [2024-05-04 16:01:37.840][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. "). biodb.INFO [2024-05-04 16:01:37.841][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:01:37.842][biodb::testThat] biodb.INFO [2024-05-04 16:01:37.850][biodb::testThat] biodb.INFO [2024-05-04 16:01:37.851][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. "). biodb.INFO [2024-05-04 16:01:37.851][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:01:37.852][biodb::testThat] biodb.DEBUG[2024-05-04 16:01:37.864][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 16:01:38.493][getUrlContent] Use RCurl 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 16:01:39.138][biodb::testThat] biodb.INFO [2024-05-04 16:01:39.139][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. "). biodb.INFO [2024-05-04 16:01:39.140][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-05-04 16:01:39.140][biodb::testThat] biodb.DEBUG[2024-05-04 16:01:40.540][getUrlContent] Use RCurl for downloading content of URL https://enzyme.expasy.org/images/1.1.1.1/image.png. biodb.TRACE[2024-05-04 16:01:40.832][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:40.833][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:40.834][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:40.835][ef$get] fields variable is a list. biodb.TRACE[2024-05-04 16:01:40.836][ef$get] Asked field names are: name. biodb.TRACE[2024-05-04 16:01:40.837][ef$get] Realnames of fields are: name. biodb.TRACE[2024-05-04 16:01:40.837][ef$get] 1 fields were returned. biodb.TRACE[2024-05-04 16:01:40.838][ef$get] fields variable is a list. biodb.INFO [2024-05-04 16:01:40.839][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2024-05-04 16:01:40.840][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler biodb.INFO [2024-05-04 16:01:40.841][self$deleteConn] Connector "expasy.enzyme" deleted. biodb.DEBUG[2024-05-04 16:01:40.842][notifyObservers] Notify observers for terminate. biodb.DEBUG[2024-05-04 16:01:40.842][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:40.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:40.844][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:40.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:40.845][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:40.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.INFO [2024-05-04 16:01:40.853][biodb::testContext] biodb.INFO [2024-05-04 16:01:40.854][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 16:01:40.855][biodb::testContext] Test context - Example long tests biodb.INFO [2024-05-04 16:01:40.855][biodb::testContext] ******************************************************************************** biodb.INFO [2024-05-04 16:01:40.865][biodb::testContext] biodb.INFO [2024-05-04 16:01:40.867][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0. biodb.DEBUG[2024-05-04 16:01:40.868][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml". biodb.DEBUG[2024-05-04 16:01:40.871][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 16:01:40.872][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2024-05-04 16:01:40.873][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2024-05-04 16:01:40.873][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:40.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:40.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:40.876][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2024-05-04 16:01:40.876][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2024-05-04 16:01:40.877][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:40.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:40.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:40.879][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2024-05-04 16:01:40.880][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2024-05-04 16:01:40.881][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:40.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:40.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:40.883][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2024-05-04 16:01:40.884][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2024-05-04 16:01:40.884][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2024-05-04 16:01:40.885][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:40.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:40.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:40.887][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2024-05-04 16:01:40.888][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2024-05-04 16:01:40.889][self$set] Set key cache.system to TRUE. biodb.DEBUG[2024-05-04 16:01:40.889][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:40.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:40.891][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:40.892][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2024-05-04 16:01:40.892][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2024-05-04 16:01:40.893][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:40.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:40.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:40.895][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2024-05-04 16:01:40.896][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2024-05-04 16:01:40.897][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2024-05-04 16:01:40.897][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:40.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:40.899][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:40.899][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2024-05-04 16:01:40.900][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2024-05-04 16:01:40.901][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:40.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:40.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:40.903][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2024-05-04 16:01:40.904][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2024-05-04 16:01:40.904][self$set] Set key force.locale to TRUE. biodb.DEBUG[2024-05-04 16:01:40.905][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:40.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:40.906][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:40.907][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2024-05-04 16:01:40.908][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2024-05-04 16:01:40.909][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2024-05-04 16:01:40.909][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2024-05-04 16:01:40.910][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2024-05-04 16:01:40.911][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2024-05-04 16:01:40.911][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:40.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:40.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:40.914][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2024-05-04 16:01:40.915][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2024-05-04 16:01:40.915][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:40.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:40.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:40.917][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2024-05-04 16:01:40.918][self$set] Set key entries.sep to "|". biodb.DEBUG[2024-05-04 16:01:40.919][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:40.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:40.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:40.921][self$getConfig()$define] Define config key offline. biodb.DEBUG[2024-05-04 16:01:40.922][self$set] Set key offline to FALSE. biodb.DEBUG[2024-05-04 16:01:40.923][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:40.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:40.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:40.925][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2024-05-04 16:01:40.926][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2024-05-04 16:01:40.927][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:40.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:40.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:40.929][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2024-05-04 16:01:40.930][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2024-05-04 16:01:40.930][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:40.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:40.932][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:40.933][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2024-05-04 16:01:40.933][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2024-05-04 16:01:40.956][self$set] Set key svn.binary.path to "". biodb.DEBUG[2024-05-04 16:01:40.957][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:40.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:40.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:40.960][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2024-05-04 16:01:40.961][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2024-05-04 16:01:40.961][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2024-05-04 16:01:40.962][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:40.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:40.964][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:40.965][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2024-05-04 16:01:40.966][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 16:01:40.967][self$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 16:01:40.968][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:01:40.969][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:01:40.970][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:01:40.970][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:01:40.971][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:01:40.972][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:01:40.973][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 16:01:40.974][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:01:40.975][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 16:01:40.975][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2024-05-04 16:01:40.976][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:01:40.977][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:40.978][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:01:40.978][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 16:01:40.978][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 16:01:40.978][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 16:01:40.978][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 16:01:40.978][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 16:01:40.979][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:01:40.980][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:01:40.981][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:01:40.982][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:01:40.982][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:01:40.987][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:01:40.988][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:01:40.989][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:40.990][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:01:40.990][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:01:40.991][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:01:40.992][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:40.993][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2024-05-04 16:01:40.994][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 16:01:40.995][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 16:01:40.996][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:01:40.996][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:01:40.997][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:01:40.998][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:01:40.999][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:01:40.999][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:01:41.000][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 16:01:41.001][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:01:41.002][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 16:01:41.002][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2024-05-04 16:01:41.003][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:01:41.004][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:41.005][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:01:41.005][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 16:01:41.005][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-05-04 16:01:41.005][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-05-04 16:01:41.005][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-05-04 16:01:41.005][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-05-04 16:01:41.006][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:01:41.007][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:01:41.008][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:01:41.009][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:01:41.009][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:01:41.010][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:01:41.011][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:01:41.012][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:41.012][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:01:41.013][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:01:41.014][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:01:41.015][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:41.016][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2024-05-04 16:01:41.017][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 16:01:41.018][self$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 16:01:41.019][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:01:41.020][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:01:41.020][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:01:41.021][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:01:41.022][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:01:41.023][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:01:41.024][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-05-04 16:01:41.024][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:01:41.025][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 16:01:41.026][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2024-05-04 16:01:41.027][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:01:41.028][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:41.028][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:01:41.029][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:41.030][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:01:41.031][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:01:41.032][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:01:41.032][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:01:41.033][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:01:41.034][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:01:41.035][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:01:41.035][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:41.036][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:01:41.037][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:01:41.038][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:01:41.039][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:41.039][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2024-05-04 16:01:41.041][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-05-04 16:01:41.042][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2024-05-04 16:01:41.042][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:01:41.043][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:01:41.044][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:01:41.045][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:01:41.046][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-05-04 16:01:41.046][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:01:41.047][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-05-04 16:01:41.048][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:01:41.049][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-05-04 16:01:41.049][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2024-05-04 16:01:41.050][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:01:41.051][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:41.052][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-05-04 16:01:41.053][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:41.053][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-05-04 16:01:41.054][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:01:41.055][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:01:41.056][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:01:41.056][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:01:41.057][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:01:41.058][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:01:41.059][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:41.059][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:01:41.060][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:01:41.061][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-05-04 16:01:41.062][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:41.063][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 16:01:41.063][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.064][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 16:01:41.065][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.066][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 16:01:41.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.068][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:41.068][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.070][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 16:01:41.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.071][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:41.072][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.073][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 16:01:41.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:41.075][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.077][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 16:01:41.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.078][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:41.079][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.080][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 16:01:41.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:41.086][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.088][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 16:01:41.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.089][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:41.090][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.091][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 16:01:41.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.093][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:41.093][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.095][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 16:01:41.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.096][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:41.097][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.098][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 16:01:41.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.100][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 16:01:41.100][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:41.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:41.104][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.105][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 16:01:41.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.107][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:41.108][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.109][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 16:01:41.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.111][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:41.111][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.113][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 16:01:41.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:41.115][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.116][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 16:01:41.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.118][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 16:01:41.118][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.120][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 16:01:41.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:41.122][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.123][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 16:01:41.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:41.125][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.127][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 16:01:41.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.128][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:41.129][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2024-05-04 16:01:41.130][self$getEntryFields()$define] Define field description. biodb.DEBUG[2024-05-04 16:01:41.131][self$getEntryFields()$define] Define field name. biodb.DEBUG[2024-05-04 16:01:41.132][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2024-05-04 16:01:41.134][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-05-04 16:01:41.135][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2024-05-04 16:01:41.136][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2024-05-04 16:01:41.137][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2024-05-04 16:01:41.138][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2024-05-04 16:01:41.139][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2024-05-04 16:01:41.140][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-05-04 16:01:41.141][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2024-05-04 16:01:41.142][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2024-05-04 16:01:41.143][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2024-05-04 16:01:41.144][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2024-05-04 16:01:41.146][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-05-04 16:01:41.147][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2024-05-04 16:01:41.148][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2024-05-04 16:01:41.149][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-05-04 16:01:41.150][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2024-05-04 16:01:41.151][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2024-05-04 16:01:41.152][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2024-05-04 16:01:41.153][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2024-05-04 16:01:41.154][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2024-05-04 16:01:41.155][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2024-05-04 16:01:41.157][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2024-05-04 16:01:41.158][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2024-05-04 16:01:41.159][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2024-05-04 16:01:41.160][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2024-05-04 16:01:41.161][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2024-05-04 16:01:41.162][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2024-05-04 16:01:41.163][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2024-05-04 16:01:41.164][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2024-05-04 16:01:41.165][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2024-05-04 16:01:41.166][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2024-05-04 16:01:41.167][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2024-05-04 16:01:41.168][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2024-05-04 16:01:41.169][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2024-05-04 16:01:41.170][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2024-05-04 16:01:41.171][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2024-05-04 16:01:41.172][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2024-05-04 16:01:41.173][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2024-05-04 16:01:41.174][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2024-05-04 16:01:41.175][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2024-05-04 16:01:41.180][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2024-05-04 16:01:41.181][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2024-05-04 16:01:41.182][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2024-05-04 16:01:41.183][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2024-05-04 16:01:41.184][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2024-05-04 16:01:41.185][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2024-05-04 16:01:41.186][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2024-05-04 16:01:41.187][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2024-05-04 16:01:41.188][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2024-05-04 16:01:41.189][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2024-05-04 16:01:41.191][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2024-05-04 16:01:41.192][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2024-05-04 16:01:41.193][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2024-05-04 16:01:41.194][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2024-05-04 16:01:41.195][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2024-05-04 16:01:41.196][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2024-05-04 16:01:41.197][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2024-05-04 16:01:41.198][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2024-05-04 16:01:41.199][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2024-05-04 16:01:41.200][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2024-05-04 16:01:41.201][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2024-05-04 16:01:41.202][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2024-05-04 16:01:41.204][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-05-04 16:01:41.205][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-05-04 16:01:41.206][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2024-05-04 16:01:41.207][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2024-05-04 16:01:41.208][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2024-05-04 16:01:41.209][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2024-05-04 16:01:41.210][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2024-05-04 16:01:41.211][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2024-05-04 16:01:41.212][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2024-05-04 16:01:41.214][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2024-05-04 16:01:41.215][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2024-05-04 16:01:41.216][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2024-05-04 16:01:41.217][self$getEntryFields()$define] Define field products. biodb.DEBUG[2024-05-04 16:01:41.218][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2024-05-04 16:01:41.219][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2024-05-04 16:01:41.220][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2024-05-04 16:01:41.222][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2024-05-04 16:01:41.223][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2024-05-04 16:01:41.224][initialize] This is biodb version 1.12.0. biodb.DEBUG[2024-05-04 16:01:41.225][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-05-04 16:01:41.225][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.226][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 16:01:41.227][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.228][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:41.228][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:41.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:41.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.231][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 16:01:41.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.233][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:41.233][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:41.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:41.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.236][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 16:01:41.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.238][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:41.238][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:41.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:41.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.241][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 16:01:41.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.243][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 16:01:41.243][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:41.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:41.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.246][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 16:01:41.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.248][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:41.248][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:41.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:41.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.251][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 16:01:41.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.253][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:41.254][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:41.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:41.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.256][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 16:01:41.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.258][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 16:01:41.259][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:41.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:41.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.262][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 16:01:41.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.263][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:41.264][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:41.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:41.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.267][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 16:01:41.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.268][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:41.269][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:41.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:41.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.276][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 16:01:41.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:41.279][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:41.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:41.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.281][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 16:01:41.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.283][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:41.284][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:41.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:41.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.286][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 16:01:41.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:41.289][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:41.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:41.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.291][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 16:01:41.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-05-04 16:01:41.294][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:41.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:41.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.297][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 16:01:41.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.298][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:41.299][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:41.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:41.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.302][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 16:01:41.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.303][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:41.304][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:41.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:41.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.307][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 16:01:41.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.308][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:41.309][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:41.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:41.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.312][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 16:01:41.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.313][FUN] Functions in observer BiodbConfig: [21]: ".__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 16:01:41.314][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-05-04 16:01:41.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:41.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:41.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.317][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 16:01:41.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.319][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 16:01:41.320][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck/biodbExpasy/definitions.yml". biodb.DEBUG[2024-05-04 16:01:41.328][self$getDbsInfo()$define] Define connector expasy.enzyme. biodb.DEBUG[2024-05-04 16:01:41.330][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-05-04 16:01:41.331][self$setPropertyValue] Setting property "description" to "Write here the description of this database.". biodb.DEBUG[2024-05-04 16:01:41.332][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-05-04 16:01:41.332][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-05-04 16:01:41.333][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-05-04 16:01:41.334][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-05-04 16:01:41.335][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2024-05-04 16:01:41.336][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-05-04 16:01:41.337][self$setPropertyValue] Setting property "entry.content.type" to "txt". biodb.DEBUG[2024-05-04 16:01:41.338][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-05-04 16:01:41.339][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-05-04 16:01:41.340][self$setPropertyValue] Setting property "name" to "Expasy ENZYME database.". biodb.DEBUG[2024-05-04 16:01:41.340][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-05-04 16:01:41.341][self$setPropertyValue] Setting property "parsing.expr" to "^ID\s+([0-9.]+)$". biodb.DEBUG[2024-05-04 16:01:41.341][self$setPropertyValue] Setting property "parsing.expr" to "^CA\s+(.+?)\.?$". biodb.DEBUG[2024-05-04 16:01:41.341][self$setPropertyValue] Setting property "parsing.expr" to "^CF\s+(.+?)\.?$". biodb.DEBUG[2024-05-04 16:01:41.341][self$setPropertyValue] Setting property "parsing.expr" to "^DE\s+(.+?)\.?$". biodb.DEBUG[2024-05-04 16:01:41.342][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2024-05-04 16:01:41.343][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-05-04 16:01:41.344][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2024-05-04 16:01:41.345][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:01:41.345][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:01:41.346][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-05-04 16:01:41.347][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-05-04 16:01:41.348][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-05-04 16:01:41.349][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-05-04 16:01:41.349][self$setPropertyValue] Setting property "urls" to "https://enzyme.expasy.org/". biodb.DEBUG[2024-05-04 16:01:41.350][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-05-04 16:01:41.351][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-05-04 16:01:41.352][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2024-05-04 16:01:41.353][self$setPropertyValue] biodb.DEBUG[2024-05-04 16:01:41.354][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2024-05-04 16:01:41.356][super$initialize] Initialize connector expasy.enzyme. biodb.DEBUG[2024-05-04 16:01:41.357][super$initialize] Register connector expasy.enzyme with the request scheduler biodb.DEBUG[2024-05-04 16:01:41.358][private$bdb$getRequestScheduler()$re ...] Register connector expasy.enzyme. biodb.DEBUG[2024-05-04 16:01:41.359][private$addConnectorRules] Create new rule for URL "enzyme.expasy.org" of connector "expasy.enzyme". biodb.DEBUG[2024-05-04 16:01:41.360][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-04 16:01:41.361][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-05-04 16:01:41.362][biodb$getFactory()$createConn] Creating new connector expasy.enzyme for database class expasy.enzyme . biodb.INFO [2024-05-04 16:01:41.363][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2024-05-04 16:01:41.364][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector expasy.enzyme from the request scheduler biodb.INFO [2024-05-04 16:01:41.365][self$deleteConn] Connector "expasy.enzyme" deleted. biodb.DEBUG[2024-05-04 16:01:41.366][notifyObservers] Notify observers for terminate. biodb.DEBUG[2024-05-04 16:01:41.366][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2024-05-04 16:01:41.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-05-04 16:01:41.368][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2024-05-04 16:01:41.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-05-04 16:01:41.369][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2024-05-04 16:01:41.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". [ FAIL 0 | WARN 0 | SKIP 0 | PASS 86 ] > > proc.time() user system elapsed 4.084 0.301 12.054
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbExpasy_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc-longtests/meat/biodbExpasy.Rcheck’ * using R version 4.4.0 beta (2024-04-14 r86421) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * 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 for sufficient/correct file permissions ... 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 ‘/Users/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)