| Back to Long Tests report for BioC 3.20 |
This page was generated on 2024-06-29 23:55 -0400 (Sat, 29 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4693 |
| palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4408 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4407 |
| 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 11/32 | Hostname | OS / Arch | CHECK | |||||||
| biodbNci 1.9.0 (landing page) Pierrick Roger
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | |||||||
| palomino6 | Windows Server 2022 Datacenter / x64 | OK | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ||||||||
|
To the developers/maintainers of the biodbNci package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: biodbNci |
| Version: 1.9.0 |
| 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 biodbNci_1.9.0.tar.gz |
| StartedAt: 2024-06-29 16:02:11 -0400 (Sat, 29 Jun 2024) |
| EndedAt: 2024-06-29 16:25:51 -0400 (Sat, 29 Jun 2024) |
| EllapsedTime: 1419.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbNci.Rcheck |
| Warnings: 0 |
biodbNci.Rcheck/tests/testthat.Rout
R version 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life"
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(biodbNci)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbNci")
biodb.INFO [2024-06-29 16:02:58.955][biodb::testContext]
biodb.INFO [2024-06-29 16:02:58.957][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-29 16:02:58.958][biodb::testContext] Test context - Generic long tests
biodb.INFO [2024-06-29 16:02:58.959][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-29 16:02:58.960][biodb::testContext]
biodb.INFO [2024-06-29 16:02:58.964][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-06-29 16:02:58.966][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-29 16:02:58.971][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-29 16:02:58.972][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-29 16:02:58.973][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-29 16:02:58.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:58.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:58.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:58.975][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-29 16:02:58.988][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-29 16:02:58.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:58.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:58.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:58.991][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-29 16:02:58.991][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-29 16:02:58.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:58.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:58.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:58.994][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-29 16:02:58.995][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-29 16:02:58.995][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-29 16:02:58.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:58.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:58.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:58.998][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-29 16:02:58.999][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-29 16:02:58.999][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-29 16:02:59.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.002][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-29 16:02:59.003][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-29 16:02:59.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.006][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-29 16:02:59.006][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-29 16:02:59.007][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-29 16:02:59.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.010][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-29 16:02:59.010][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-29 16:02:59.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.013][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-29 16:02:59.014][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-29 16:02:59.014][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-29 16:02:59.015][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.017][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-29 16:02:59.018][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-29 16:02:59.018][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-29 16:02:59.019][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-29 16:02:59.020][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-29 16:02:59.020][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-29 16:02:59.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.023][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-29 16:02:59.024][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-29 16:02:59.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.026][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-29 16:02:59.027][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-29 16:02:59.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.030][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-29 16:02:59.030][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-29 16:02:59.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.033][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-29 16:02:59.034][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-29 16:02:59.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.036][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[2024-06-29 16:02:59.036][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-29 16:02:59.037][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-29 16:02:59.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.040][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-29 16:02:59.040][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-29 16:02:59.056][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-29 16:02:59.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.058][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-29 16:02:59.059][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-29 16:02:59.060][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-29 16:02:59.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.064][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-29 16:02:59.087][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:59.102][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-06-29 16:02:59.103][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:59.104][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:02:59.105][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:59.105][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:02:59.106][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:59.107][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:02:59.108][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-29 16:02:59.108][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:02:59.109][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:59.110][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-29 16:02:59.110][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:02:59.111][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:59.112][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:59.113][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-29 16:02:59.113][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-29 16:02:59.113][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-29 16:02:59.113][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-29 16:02:59.113][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-29 16:02:59.113][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:02:59.114][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:59.115][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:59.115][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:02:59.116][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:59.117][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:59.117][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:02:59.118][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:59.119][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:02:59.119][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:02:59.120][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:59.121][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:59.122][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-29 16:02:59.123][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:59.124][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-29 16:02:59.124][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:59.125][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:02:59.126][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:59.126][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:02:59.127][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:59.128][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:02:59.128][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-29 16:02:59.129][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:02:59.130][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:59.131][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-29 16:02:59.131][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:02:59.132][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:59.133][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:59.133][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-29 16:02:59.133][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-29 16:02:59.133][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-29 16:02:59.133][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-29 16:02:59.133][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-29 16:02:59.134][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:02:59.135][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:59.136][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:59.136][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:02:59.137][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:59.138][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:59.138][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:02:59.139][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:59.140][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:02:59.140][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:02:59.141][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:59.142][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:59.142][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-29 16:02:59.144][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:59.144][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-06-29 16:02:59.145][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:59.146][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:02:59.146][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:59.147][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:02:59.148][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:59.149][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:02:59.149][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-29 16:02:59.150][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:02:59.151][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:59.151][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-29 16:02:59.152][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:02:59.153][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:59.154][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:59.154][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:59.155][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:02:59.156][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:59.156][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:59.157][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:02:59.158][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:59.158][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:59.159][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:02:59.160][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:59.160][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:02:59.161][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:02:59.162][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:59.163][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:59.164][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-29 16:02:59.165][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:59.166][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-29 16:02:59.166][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:59.167][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:02:59.168][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:59.168][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:02:59.169][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:59.170][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:02:59.171][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-29 16:02:59.171][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:02:59.172][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:59.173][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-29 16:02:59.174][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:02:59.174][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:59.175][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:59.176][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:59.176][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:02:59.177][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:59.178][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:59.178][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:02:59.179][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:59.180][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:59.181][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:02:59.182][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:59.182][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:02:59.183][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:02:59.184][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:59.184][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:59.187][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-29 16:02:59.188][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.194][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.196][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.205][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.218][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.233][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[2024-06-29 16:02:59.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.240][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.243][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[2024-06-29 16:02:59.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.247][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-29 16:02:59.250][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-29 16:02:59.251][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-29 16:02:59.252][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-29 16:02:59.253][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-29 16:02:59.254][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-29 16:02:59.255][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-29 16:02:59.256][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-29 16:02:59.257][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-29 16:02:59.258][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-29 16:02:59.259][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-29 16:02:59.260][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-29 16:02:59.261][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-29 16:02:59.262][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-29 16:02:59.263][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-29 16:02:59.264][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-29 16:02:59.265][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-29 16:02:59.266][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-29 16:02:59.267][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-29 16:02:59.268][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-29 16:02:59.269][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-29 16:02:59.270][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-29 16:02:59.271][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-29 16:02:59.272][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-29 16:02:59.273][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-29 16:02:59.274][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-29 16:02:59.275][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-29 16:02:59.276][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-29 16:02:59.277][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-29 16:02:59.278][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-29 16:02:59.279][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-29 16:02:59.280][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-29 16:02:59.281][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-29 16:02:59.282][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-29 16:02:59.283][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-29 16:02:59.283][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-29 16:02:59.284][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-29 16:02:59.285][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-29 16:02:59.286][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-29 16:02:59.287][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-29 16:02:59.288][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-29 16:02:59.290][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-29 16:02:59.291][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-29 16:02:59.292][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-29 16:02:59.293][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-29 16:02:59.294][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-29 16:02:59.295][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-29 16:02:59.296][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-29 16:02:59.297][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-29 16:02:59.297][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-29 16:02:59.298][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-29 16:02:59.299][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-29 16:02:59.300][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-29 16:02:59.301][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-29 16:02:59.302][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-29 16:02:59.303][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-29 16:02:59.304][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-29 16:02:59.305][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-29 16:02:59.306][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-29 16:02:59.308][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-29 16:02:59.309][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-29 16:02:59.310][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-29 16:02:59.311][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-29 16:02:59.312][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-29 16:02:59.313][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-29 16:02:59.314][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-29 16:02:59.315][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-29 16:02:59.316][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-29 16:02:59.317][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-29 16:02:59.318][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-29 16:02:59.319][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-29 16:02:59.320][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-29 16:02:59.321][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-29 16:02:59.322][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-29 16:02:59.323][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-29 16:02:59.324][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-29 16:02:59.325][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-29 16:02:59.326][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-29 16:02:59.327][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-29 16:02:59.328][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-29 16:02:59.329][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-29 16:02:59.330][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-29 16:02:59.331][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-29 16:02:59.335][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-29 16:02:59.336][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-06-29 16:02:59.339][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-29 16:02:59.339][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.340][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:59.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:59.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:59.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:59.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:59.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:59.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.362][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:59.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:59.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:59.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:59.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:59.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:59.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:59.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:59.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:59.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:59.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:59.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:59.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:59.390][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:59.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:59.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:59.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:59.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:59.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:59.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:59.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:59.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:59.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:59.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:59.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.416][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:59.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:59.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:02:59.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:59.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:59.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:02:59.426][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-06-29 16:02:59.433][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-06-29 16:02:59.434][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:59.435][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-06-29 16:02:59.436][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:59.437][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:02:59.437][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:59.438][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-06-29 16:02:59.439][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:59.440][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:02:59.440][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-06-29 16:02:59.441][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:02:59.442][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:59.442][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-06-29 16:02:59.443][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:02:59.444][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-06-29 16:02:59.444][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-06-29 16:02:59.444][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-06-29 16:02:59.444][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-06-29 16:02:59.444][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-06-29 16:02:59.444][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-06-29 16:02:59.444][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-06-29 16:02:59.445][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-29 16:02:59.445][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:59.446][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-29 16:02:59.447][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:59.448][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:59.448][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:02:59.449][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:02:59.450][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:02:59.450][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:02:59.451][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-06-29 16:02:59.451][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-06-29 16:02:59.451][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-06-29 16:02:59.451][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-06-29 16:02:59.452][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:02:59.452][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:02:59.453][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-29 16:02:59.454][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:02:59.458][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-06-29 16:02:59.476][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-06-29 16:02:59.477][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-06-29 16:02:59.480][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-06-29 16:02:59.483][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-06-29 16:02:59.486][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-29 16:02:59.487][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-29 16:02:59.488][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-29 16:02:59.489][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-29 16:02:59.490][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-29 16:02:59.490][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-06-29 16:02:59.523][biodb::testThat]
biodb.INFO [2024-06-29 16:02:59.524][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-06-29 16:02:59.525][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:02:59.526][biodb::testThat]
biodb.TRACE[2024-06-29 16:02:59.528][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-749674-content.sdf".
biodb.DEBUG[2024-06-29 16:02:59.529][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-06-29 16:02:59.532][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-06-29 16:02:59.538][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-29 16:02:59.539][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:59.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:59.550][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.551][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.552][FUN] Functions in observer BiodbConfig: [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[2024-06-29 16:02:59.565][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:59.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:59.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:59.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:59.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.580][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:02:59.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:02:59.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.600][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:02:59.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:02:59.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.603][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:02:59.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:02:59.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.606][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:02:59.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:02:59.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.609][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:02:59.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:02:59.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.612][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:02:59.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:02:59.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.615][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:02:59.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:02:59.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.618][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:02:59.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:02:59.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.622][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:02:59.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:02:59.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.624][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:02:59.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:02:59.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:59.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:59.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.630][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:02:59.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:02:59.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:59.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:59.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:59.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:59.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:59.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:59.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:59.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:59.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:59.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:59.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:59.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:59.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-29 16:02:59.678][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 749674.
biodb.TRACE[2024-06-29 16:02:59.680][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:02:59.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:02:59.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.683][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:02:59.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:02:59.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.685][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-29 16:02:59.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-29 16:02:59.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.688][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-29 16:02:59.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-29 16:02:59.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:59.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:59.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.716][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:02:59.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:02:59.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:59.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:59.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:59.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:59.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:59.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:59.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.732][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:59.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:59.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:59.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:59.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:59.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:59.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.741][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:02:59.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:02:59.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.745][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:02:59.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:02:59.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.748][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:02:59.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:02:59.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:59.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:59.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:59.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:59.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:59.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:59.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.769][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:59.770][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:59.771][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.772][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:59.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:59.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.782][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:02:59.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:02:59.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.785][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:02:59.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:02:59.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.788][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:02:59.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:02:59.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.791][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:02:59.791][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:02:59.792][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.793][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.794][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:02:59.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:02:59.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.803][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:02:59.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:02:59.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.806][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:02:59.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:02:59.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.809][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:02:59.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:02:59.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.812][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:02:59.812][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:02:59.813][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.814][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.814][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:02:59.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:02:59.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.824][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:02:59.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:02:59.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.827][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:02:59.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:02:59.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.830][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:02:59.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:02:59.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.833][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:02:59.833][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:02:59.834][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.835][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.836][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:02:59.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:02:59.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.845][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:02:59.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:02:59.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.848][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:02:59.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:02:59.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.851][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:02:59.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:02:59.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.854][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:02:59.855][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:02:59.856][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.856][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.857][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:02:59.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:02:59.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.867][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:59.868][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:59.868][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.869][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.877][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:02:59.878][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:02:59.878][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.879][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.883][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:02:59.884][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:02:59.884][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.885][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.889][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:02:59.890][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:02:59.890][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.891][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.895][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:02:59.896][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:02:59.896][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.897][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.909][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/testref/entry-nci.cactus-750690-content.sdf".
biodb.DEBUG[2024-06-29 16:02:59.933][biodb$getFactory()$createEntryFromCo ...] Creating NCI CACTUS entries from 1 content(s).
biodb.DEBUG[2024-06-29 16:02:59.934][biodb$getFactory()$createEntryFromCo ...] Parsing 1 NCI CACTUS entries.
biodb.DEBUG[2024-06-29 16:02:59.936][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-29 16:02:59.936][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:02:59.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:02:59.941][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:02:59.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:02:59.942][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:02:59.943][FUN] Functions in observer BiodbConfig: [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[2024-06-29 16:02:59.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:59.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:59.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:02:59.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:02:59.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.969][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-29 16:02:59.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-29 16:02:59.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.975][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-29 16:02:59.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-29 16:02:59.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.979][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:02:59.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:02:59.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.981][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:02:59.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:02:59.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.985][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:02:59.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:02:59.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.987][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:02:59.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:02:59.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.990][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:59.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:59.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.993][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:59.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:59.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.996][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:02:59.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:02:59.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:02:59.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:02:59.999][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:03:00.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:03:00.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.002][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:03:00.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:03:00.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.005][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:03:00.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:03:00.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.008][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:03:00.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:03:00.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.011][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:03:00.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:03:00.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.014][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:03:00.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:03:00.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.017][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:03:00.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:03:00.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.020][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:03:00.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:03:00.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.023][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:03:00.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:03:00.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.026][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:03:00.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:03:00.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:03:00.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:03:00.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.032][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:03:00.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:03:00.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:03:00.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:03:00.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:03:00.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:03:00.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:03:00.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:03:00.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:03:00.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:03:00.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:03:00.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:03:00.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:03:00.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:03:00.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-29 16:03:00.052][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 750690.
biodb.TRACE[2024-06-29 16:03:00.067][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:03:00.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:03:00.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.070][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:03:00.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:03:00.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.073][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-29 16:03:00.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-29 16:03:00.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.076][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-29 16:03:00.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-29 16:03:00.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:03:00.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:03:00.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.089][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:03:00.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:03:00.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.095][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:03:00.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:03:00.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:03:00.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:03:00.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:03:00.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:03:00.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:03:00.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:03:00.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:03:00.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:03:00.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:03:00.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:03:00.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.114][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:03:00.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:03:00.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.117][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:03:00.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:03:00.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.120][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:03:00.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:03:00.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:03:00.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:03:00.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:03:00.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:03:00.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:03:00.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:03:00.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.144][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:03:00.145][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:03:00.146][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.147][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:03:00.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:03:00.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.157][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-29 16:03:00.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-29 16:03:00.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.160][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-29 16:03:00.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-29 16:03:00.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.163][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-29 16:03:00.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-29 16:03:00.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.166][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-29 16:03:00.166][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-29 16:03:00.167][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.168][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.168][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-29 16:03:00.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-29 16:03:00.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.177][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:03:00.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:03:00.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.180][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:03:00.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:03:00.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.183][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:03:00.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:03:00.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.186][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:03:00.187][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:03:00.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.188][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.189][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:03:00.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:03:00.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.202][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:03:00.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:03:00.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.205][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:03:00.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:03:00.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.208][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:03:00.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:03:00.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.211][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:03:00.212][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:03:00.212][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.213][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.214][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:03:00.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:03:00.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.223][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:03:00.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:03:00.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.226][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:03:00.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:03:00.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.229][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:03:00.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:03:00.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.232][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:03:00.233][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:03:00.234][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.234][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.235][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:03:00.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:03:00.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.244][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:03:00.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:03:00.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.248][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:03:00.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:03:00.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.251][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:03:00.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:03:00.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.254][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:03:00.255][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:03:00.255][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.256][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.257][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:03:00.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:03:00.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.266][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:03:00.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:03:00.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.269][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:03:00.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:03:00.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.272][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:03:00.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:03:00.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.275][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:03:00.276][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:03:00.277][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.277][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.278][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:03:00.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:03:00.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.288][ef$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:03:00.288][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:03:00.289][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.290][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.294][ef$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-29 16:03:00.295][ef$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-29 16:03:00.295][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.296][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.300][ef$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:03:00.301][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:03:00.301][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.302][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.306][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:03:00.307][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:03:00.307][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.308][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.316][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:03:00.316][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:03:00.317][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.318][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.322][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:03:00.322][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:03:00.323][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.324][ef$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:03:00.328][ef$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:03:00.328][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:03:00.329][ef$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:03:00.330][ef$get] fields variable is a list.
biodb.INFO [2024-06-29 16:03:00.336][biodb::testThat]
biodb.INFO [2024-06-29 16:03:00.337][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-06-29 16:03:00.338][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:03:00.338][biodb::testThat]
biodb.DEBUG[2024-06-29 16:03:00.340][private$loadEntries] Creating entries from ids [2]: "749674, 750690".
biodb.DEBUG[2024-06-29 16:03:00.345][conn$getEntryContent] Get NCI CACTUS entry content(s) for 2 id(s)...
biodb.DEBUG[2024-06-29 16:03:00.348][self$isDownloaded] Database nci.cactus has not yet been downloaded.
biodb.INFO [2024-06-29 16:03:00.349][self$download] Downloading whole database of nci.cactus.
biodb.INFO [2024-06-29 16:03:00.350][private$doDownload] Downloading NCI CACTUS database at "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz" ...
biodb.DEBUG[2024-06-29 16:03:00.351][sched$downloadFile] Downloading file "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
trying URL 'https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz'
Content type 'application/x-gzip' length 206737123 bytes (197.2 MB)
==================================================
downloaded 197.2 MB
biodb.TRACE[2024-06-29 16:03:31.082][cch$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/nci.cactus6427642ca638gz".
biodb.TRACE[2024-06-29 16:03:31.083][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2024-06-29 16:03:31.084][cch$addFilesToCache] Done adding files.
biodb.DEBUG[2024-06-29 16:03:31.085][self$getDownloadPath] Download path of nci.cactus is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2024-06-29 16:03:31.086][self$download] Downloading of nci.cactus completed.
biodb.TRACE[2024-06-29 16:03:31.087][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/marker64272f54d9e9marker".
biodb.TRACE[2024-06-29 16:03:31.088][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/downloaded.marker".
biodb.DEBUG[2024-06-29 16:03:31.089][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-06-29 16:03:31.090][self$isDownloaded] Database nci.cactus has already been downloaded.
biodb.INFO [2024-06-29 16:03:31.091][self$download] Extract whole database of nci.cactus.
biodb.INFO [2024-06-29 16:03:31.092][private$doExtractDownload] Extracting content of downloaded biodbNci, a library for connecting to the National Cancer Institute (USA) CACTUS Database....
biodb.DEBUG[2024-06-29 16:03:31.093][self$getDownloadPath] Download path of nci.cactus is "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/download.gz".
biodb.DEBUG[2024-06-29 16:04:27.666][private$doExtractDownload] Delete existing entry files in cache system.
biodb.DEBUG[2024-06-29 16:04:27.686][private$doExtractDownload] Extract single entries from downloaded file "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/cactus_rdfs", into "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp".
biodb.TRACE[2024-06-29 16:24:04.426][self$addFilesToCache] Moving files to cache [265242]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_1.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_2.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_3.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_4.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_5.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_6.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_7.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_8.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_9.txt, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/entry_10.txt, ...".
biodb.TRACE[2024-06-29 16:24:04.747][private$doAddFilesToCache] Destination files are [265242]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/1.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/2.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/3.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/4.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/5.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/6.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/7.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/8.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/9.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/10.sdf, ...".
biodb.DEBUG[2024-06-29 16:25:45.539][self$addFilesToCache] Done adding files.
biodb.DEBUG[2024-06-29 16:25:45.540][private$doExtractDownload] Delete extracted database.
biodb.TRACE[2024-06-29 16:25:45.573][self$addFilesToCache] Moving files to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/tmp/marker64276bae6845marker".
biodb.TRACE[2024-06-29 16:25:45.574][private$doAddFilesToCache] Destination files are [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/extracted.marker".
biodb.DEBUG[2024-06-29 16:25:45.575][self$addFilesToCache] Done adding files.
biodb.TRACE[2024-06-29 16:25:45.576][cch$loadFileContent] Trying to load 2 files from cache: [2]: "749674, 750690".
biodb.TRACE[2024-06-29 16:25:45.577][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-06-29 16:25:45.615][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/749674.sdf, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/nci.cactus-8efc65070d01b214e760b1d4932ee427/750690.sdf".
biodb.DEBUG[2024-06-29 16:25:46.490][conn$getEntryContent] 2 NCI CACTUS entry content(s) loaded from cache.
biodb.DEBUG[2024-06-29 16:25:46.491][self$createEntryFromContent] Creating NCI CACTUS entries from 2 content(s).
biodb.DEBUG[2024-06-29 16:25:46.492][self$createEntryFromContent] Parsing 2 NCI CACTUS entries.
biodb.DEBUG[2024-06-29 16:25:46.493][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-29 16:25:46.494][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:25:46.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:25:46.525][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:46.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:46.526][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:46.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-29 16:25:46.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:25:46.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:25:46.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:25:46.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:25:46.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.538][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:25:46.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:25:46.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.541][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:25:46.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:25:46.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.544][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:25:46.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:25:46.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.547][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:25:46.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:25:46.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.550][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:25:46.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:25:46.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.553][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:25:46.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:25:46.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.556][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:25:46.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:25:46.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.559][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:25:46.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:25:46.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.563][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:25:46.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:25:46.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.566][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:25:46.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:25:46.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:25:46.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:25:46.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.572][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:25:46.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:25:46.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:25:46.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:25:46.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:25:46.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:25:46.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:25:46.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:25:46.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-29 16:25:46.585][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-06-29 16:25:46.585][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:25:46.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:25:46.590][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:46.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:46.592][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:46.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-06-29 16:25:46.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:25:46.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:25:46.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:25:46.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:25:46.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.605][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-29 16:25:46.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-29 16:25:46.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.608][self$getBiodb()$getEntryFields()$get] Asked field names are: cas.id.
biodb.TRACE[2024-06-29 16:25:46.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: cas.id.
biodb.TRACE[2024-06-29 16:25:46.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.611][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:25:46.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:25:46.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.614][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-06-29 16:25:46.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-06-29 16:25:46.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.617][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:25:46.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:25:46.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.620][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-06-29 16:25:46.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-06-29 16:25:46.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.623][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:25:46.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:25:46.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.626][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:25:46.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:25:46.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.629][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:25:46.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:25:46.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.632][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:25:46.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:25:46.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.635][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:25:46.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:25:46.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.638][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:25:46.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:25:46.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.640][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-06-29 16:25:46.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-06-29 16:25:46.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.644][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:25:46.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:25:46.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.647][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-06-29 16:25:46.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-06-29 16:25:46.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.650][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:25:46.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:25:46.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.653][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-06-29 16:25:46.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-06-29 16:25:46.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.656][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:25:46.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:25:46.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.659][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:25:46.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:25:46.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:25:46.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:25:46.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.665][self$getBiodb()$getEntryFields()$get] Asked field names are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:25:46.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nci.cactus.id.
biodb.TRACE[2024-06-29 16:25:46.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:25:46.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:25:46.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:25:46.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:25:46.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:25:46.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:25:46.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:25:46.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:25:46.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:25:46.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:25:46.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:25:46.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:25:46.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:25:46.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:25:46.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:25:46.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:25:46.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-06-29 16:25:46.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-06-29 16:25:46.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-06-29 16:25:46.693][self$createEntryFromContent] Accession numbers: 749674, 750690.
biodb.TRACE[2024-06-29 16:25:46.694][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-29 16:25:46.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-29 16:25:46.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.697][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-29 16:25:46.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-29 16:25:46.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.699][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-29 16:25:46.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-29 16:25:46.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.707][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-06-29 16:25:46.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-06-29 16:25:46.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.710][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-06-29 16:25:46.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-06-29 16:25:46.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.713][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-06-29 16:25:46.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-06-29 16:25:46.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-29 16:25:46.722][biodb::testThat]
biodb.INFO [2024-06-29 16:25:46.723][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-06-29 16:25:46.724][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:25:46.724][biodb::testThat]
biodb.INFO [2024-06-29 16:25:46.729][biodb::testThat]
biodb.INFO [2024-06-29 16:25:46.730][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-06-29 16:25:46.731][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:25:46.731][biodb::testThat]
biodb.WARN [2024-06-29 16:25:46.745][self$searchForEntries] This database is not searchable by field "name".
biodb.WARN [2024-06-29 16:25:46.759][self$searchForEntries] This database is not searchable by field "name".
biodb.INFO [2024-06-29 16:25:46.767][biodb::testThat]
biodb.INFO [2024-06-29 16:25:46.768][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-06-29 16:25:46.768][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:25:46.769][biodb::testThat]
biodb.TRACE[2024-06-29 16:25:46.912][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:25:46.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:25:46.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.916][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:25:46.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:25:46.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.919][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-29 16:25:46.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-29 16:25:46.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.922][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-29 16:25:46.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-29 16:25:46.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.968][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:25:46.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:25:46.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.972][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-06-29 16:25:46.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-06-29 16:25:46.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.975][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-06-29 16:25:46.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-06-29 16:25:46.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-06-29 16:25:46.977][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-06-29 16:25:46.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-06-29 16:25:46.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-06-29 16:25:46.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-06-29 16:25:47.040][biodb::testThat]
biodb.INFO [2024-06-29 16:25:47.041][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-06-29 16:25:47.042][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:25:47.042][biodb::testThat]
biodb.INFO [2024-06-29 16:25:47.049][biodb::testThat]
biodb.INFO [2024-06-29 16:25:47.050][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-06-29 16:25:47.050][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:25:47.051][biodb::testThat]
biodb.INFO [2024-06-29 16:25:47.057][biodb::testThat]
biodb.INFO [2024-06-29 16:25:47.058][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-06-29 16:25:47.059][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:25:47.059][biodb::testThat]
biodb.INFO [2024-06-29 16:25:47.065][biodb::testThat]
biodb.INFO [2024-06-29 16:25:47.066][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-06-29 16:25:47.066][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-06-29 16:25:47.067][biodb::testThat]
biodb.INFO [2024-06-29 16:25:47.072][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-29 16:25:47.073][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-06-29 16:25:47.074][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-06-29 16:25:47.075][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-29 16:25:47.075][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:25:47.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:25:47.076][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:47.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:47.078][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:47.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-06-29 16:25:47.086][biodb::testContext]
biodb.INFO [2024-06-29 16:25:47.087][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-29 16:25:47.088][biodb::testContext] Test context - Example long tests
biodb.INFO [2024-06-29 16:25:47.088][biodb::testContext] ********************************************************************************
biodb.INFO [2024-06-29 16:25:47.089][biodb::testContext]
biodb.INFO [2024-06-29 16:25:47.092][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-06-29 16:25:47.095][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-06-29 16:25:47.098][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-29 16:25:47.099][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-06-29 16:25:47.100][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-06-29 16:25:47.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:47.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:47.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:47.103][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-06-29 16:25:47.103][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-06-29 16:25:47.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:47.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:47.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:47.106][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-06-29 16:25:47.107][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-06-29 16:25:47.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:47.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:47.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:47.110][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-06-29 16:25:47.111][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-06-29 16:25:47.112][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-06-29 16:25:47.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:47.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:47.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:47.115][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-06-29 16:25:47.116][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-06-29 16:25:47.117][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-06-29 16:25:47.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:47.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:47.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:47.120][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-06-29 16:25:47.121][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-06-29 16:25:47.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:47.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:47.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:47.124][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-06-29 16:25:47.124][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-06-29 16:25:47.125][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-06-29 16:25:47.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:47.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:47.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:47.128][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-06-29 16:25:47.128][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-06-29 16:25:47.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:47.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:47.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:47.131][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-06-29 16:25:47.132][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-06-29 16:25:47.133][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-06-29 16:25:47.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:47.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:47.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:47.135][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-06-29 16:25:47.136][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-06-29 16:25:47.137][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-06-29 16:25:47.138][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-06-29 16:25:47.139][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-06-29 16:25:47.139][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-06-29 16:25:47.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:47.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:47.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:47.142][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-06-29 16:25:47.143][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-06-29 16:25:47.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:47.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:47.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:47.146][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-06-29 16:25:47.146][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-06-29 16:25:47.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:47.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:47.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:47.149][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-06-29 16:25:47.150][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-06-29 16:25:47.150][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:47.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:47.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:47.152][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-06-29 16:25:47.153][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-06-29 16:25:47.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:47.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:47.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:47.156][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-06-29 16:25:47.157][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-06-29 16:25:47.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:47.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:47.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:47.160][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-06-29 16:25:47.160][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-06-29 16:25:48.467][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-06-29 16:25:48.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.470][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-06-29 16:25:48.471][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-06-29 16:25:48.472][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-06-29 16:25:48.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.475][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-06-29 16:25:48.476][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:25:48.476][self$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[2024-06-29 16:25:48.477][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:25:48.478][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:25:48.479][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:25:48.479][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:25:48.480][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:25:48.481][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:25:48.482][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-29 16:25:48.483][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:25:48.483][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:25:48.484][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-06-29 16:25:48.485][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:25:48.485][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:25:48.486][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:25:48.487][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-29 16:25:48.487][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-29 16:25:48.487][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-29 16:25:48.487][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-29 16:25:48.487][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-29 16:25:48.487][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:25:48.488][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:25:48.489][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:25:48.489][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:25:48.490][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:25:48.491][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:25:48.491][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:25:48.492][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:25:48.493][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:25:48.493][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:25:48.494][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:25:48.495][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:25:48.496][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-06-29 16:25:48.497][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:25:48.498][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-06-29 16:25:48.498][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:25:48.499][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:25:48.500][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:25:48.500][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:25:48.501][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:25:48.502][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:25:48.502][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-29 16:25:48.503][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:25:48.504][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:25:48.505][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-06-29 16:25:48.505][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:25:48.506][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:25:48.507][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:25:48.507][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-06-29 16:25:48.507][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-06-29 16:25:48.507][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-06-29 16:25:48.507][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-06-29 16:25:48.507][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-06-29 16:25:48.508][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:25:48.509][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:25:48.509][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:25:48.510][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:25:48.511][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:25:48.511][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:25:48.512][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:25:48.513][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:25:48.514][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:25:48.514][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:25:48.515][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:25:48.515][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:25:48.516][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-06-29 16:25:48.518][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:25:48.518][self$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[2024-06-29 16:25:48.519][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:25:48.520][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:25:48.521][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:25:48.521][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:25:48.522][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:25:48.523][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:25:48.524][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-06-29 16:25:48.524][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:25:48.525][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:25:48.526][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-06-29 16:25:48.527][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:25:48.528][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:25:48.528][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:25:48.529][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:25:48.530][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:25:48.531][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:25:48.531][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:25:48.532][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:25:48.533][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:25:48.534][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:25:48.534][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:25:48.535][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:25:48.536][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:25:48.537][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:25:48.537][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:25:48.538][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:25:48.539][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-06-29 16:25:48.540][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:25:48.541][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-06-29 16:25:48.541][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:25:48.542][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:25:48.543][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-06-29 16:25:48.544][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-06-29 16:25:48.544][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-06-29 16:25:48.545][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:25:48.546][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-06-29 16:25:48.546][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:25:48.547][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:25:48.548][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-06-29 16:25:48.548][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:25:48.549][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:25:48.550][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-06-29 16:25:48.551][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:25:48.551][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-06-29 16:25:48.552][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:25:48.552][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:25:48.553][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:25:48.554][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:25:48.554][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:25:48.555][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:25:48.556][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:25:48.556][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:25:48.557][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:25:48.558][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-06-29 16:25:48.559][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:25:48.560][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-29 16:25:48.560][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.563][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.574][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.616][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-06-29 16:25:48.617][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-06-29 16:25:48.618][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-06-29 16:25:48.619][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-06-29 16:25:48.620][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-06-29 16:25:48.621][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-06-29 16:25:48.622][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-06-29 16:25:48.623][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-06-29 16:25:48.624][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-06-29 16:25:48.625][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-06-29 16:25:48.625][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-06-29 16:25:48.626][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-06-29 16:25:48.627][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-06-29 16:25:48.628][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-06-29 16:25:48.629][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-06-29 16:25:48.630][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-06-29 16:25:48.631][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-06-29 16:25:48.632][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-06-29 16:25:48.633][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-06-29 16:25:48.634][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-06-29 16:25:48.635][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-06-29 16:25:48.636][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-06-29 16:25:48.637][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-06-29 16:25:48.638][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-06-29 16:25:48.639][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-06-29 16:25:48.640][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-06-29 16:25:48.641][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-06-29 16:25:48.642][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-06-29 16:25:48.643][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-06-29 16:25:48.644][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-06-29 16:25:48.645][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-06-29 16:25:48.646][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-06-29 16:25:48.647][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-06-29 16:25:48.648][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-06-29 16:25:48.649][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-06-29 16:25:48.650][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-06-29 16:25:48.651][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-06-29 16:25:48.652][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-06-29 16:25:48.652][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-06-29 16:25:48.653][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-06-29 16:25:48.654][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-06-29 16:25:48.655][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-06-29 16:25:48.656][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-06-29 16:25:48.657][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-06-29 16:25:48.658][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-06-29 16:25:48.659][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-06-29 16:25:48.660][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-06-29 16:25:48.661][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-06-29 16:25:48.662][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-06-29 16:25:48.663][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-06-29 16:25:48.664][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-06-29 16:25:48.665][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-06-29 16:25:48.666][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-06-29 16:25:48.667][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-06-29 16:25:48.668][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-06-29 16:25:48.669][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-06-29 16:25:48.670][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-06-29 16:25:48.671][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-06-29 16:25:48.672][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-06-29 16:25:48.673][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-06-29 16:25:48.674][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-06-29 16:25:48.675][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-06-29 16:25:48.676][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-06-29 16:25:48.677][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-06-29 16:25:48.678][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-06-29 16:25:48.679][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-06-29 16:25:48.680][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-06-29 16:25:48.681][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-06-29 16:25:48.682][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-06-29 16:25:48.683][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-06-29 16:25:48.684][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-06-29 16:25:48.685][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-06-29 16:25:48.686][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-06-29 16:25:48.687][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-06-29 16:25:48.688][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-06-29 16:25:48.689][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-06-29 16:25:48.690][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-06-29 16:25:48.691][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-06-29 16:25:48.692][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-06-29 16:25:48.693][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-06-29 16:25:48.693][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-06-29 16:25:48.694][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-06-29 16:25:48.695][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-06-29 16:25:48.696][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-06-29 16:25:48.698][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-06-29 16:25:48.698][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-06-29 16:25:48.699][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.700][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:25:48.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:25:48.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:25:48.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:25:48.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:25:48.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:25:48.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:25:48.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:25:48.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:25:48.720][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:25:48.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:25:48.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:25:48.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:25:48.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:25:48.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:25:48.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:25:48.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:25:48.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:25:48.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:25:48.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:25:48.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.745][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:25:48.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:25:48.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:25:48.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:25:48.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:25:48.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:25:48.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:25:48.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:25:48.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:25:48.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:25:48.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:25:48.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:25:48.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-06-29 16:25:48.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:25:48.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:25:48.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-06-29 16:25:48.902][biodb$loadDefinitions] Load definitions from file "/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/biodbNci/definitions.yml".
biodb.DEBUG[2024-06-29 16:25:48.925][self$getDbsInfo()$define] Define connector nci.cactus.
biodb.DEBUG[2024-06-29 16:25:48.927][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-06-29 16:25:48.927][self$setPropertyValue] Setting property "description" to "National Cancer Institute (USA) CACTUS Database.".
biodb.DEBUG[2024-06-29 16:25:48.928][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-06-29 16:25:48.929][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-06-29 16:25:48.930][self$setPropertyValue] Setting property "downloadable" to "TRUE".
biodb.DEBUG[2024-06-29 16:25:48.931][self$setPropertyValue] Setting property "dwnld.ext" to "gz".
biodb.DEBUG[2024-06-29 16:25:48.931][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-06-29 16:25:48.932][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-06-29 16:25:48.933][self$setPropertyValue] Setting property "entry.content.type" to "sdf".
biodb.DEBUG[2024-06-29 16:25:48.934][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-06-29 16:25:48.935][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-06-29 16:25:48.936][self$setPropertyValue] Setting property "name" to "NCI CACTUS".
biodb.DEBUG[2024-06-29 16:25:48.936][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-06-29 16:25:48.937][self$setPropertyValue] Setting property "parsing.expr" to "NSC".
biodb.DEBUG[2024-06-29 16:25:48.937][self$setPropertyValue] Setting property "parsing.expr" to "DTP names".
biodb.DEBUG[2024-06-29 16:25:48.937][self$setPropertyValue] Setting property "parsing.expr" to "Standard InChI".
biodb.DEBUG[2024-06-29 16:25:48.937][self$setPropertyValue] Setting property "parsing.expr" to "c("Standard InChIKey", "^InChIKey=(.*)$")".
biodb.DEBUG[2024-06-29 16:25:48.937][self$setPropertyValue] Setting property "parsing.expr" to "Formula".
biodb.DEBUG[2024-06-29 16:25:48.937][self$setPropertyValue] Setting property "parsing.expr" to "Molecular Weight".
biodb.DEBUG[2024-06-29 16:25:48.937][self$setPropertyValue] Setting property "parsing.expr" to "CAS".
biodb.DEBUG[2024-06-29 16:25:48.938][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-06-29 16:25:48.939][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:25:48.940][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-06-29 16:25:48.941][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:25:48.941][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:25:48.942][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-06-29 16:25:48.943][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-06-29 16:25:48.943][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-06-29 16:25:48.944][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-06-29 16:25:48.945][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-06-29 16:25:48.945][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/".
biodb.DEBUG[2024-06-29 16:25:48.945][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/".
biodb.DEBUG[2024-06-29 16:25:48.945][self$setPropertyValue] Setting property "urls" to "https://cactus.nci.nih.gov/download/nci/NCI-Open_2012-05-01.sdf.gz".
biodb.DEBUG[2024-06-29 16:25:48.946][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-06-29 16:25:48.946][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-06-29 16:25:48.947][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-06-29 16:25:48.948][self$setPropertyValue]
biodb.DEBUG[2024-06-29 16:25:48.949][self$getEntryFields()$define] Define field nci.cactus.id.
biodb.DEBUG[2024-06-29 16:25:48.951][super$initialize] Initialize connector nci.cactus.
biodb.DEBUG[2024-06-29 16:25:48.952][super$initialize] Register connector nci.cactus with the request scheduler
biodb.DEBUG[2024-06-29 16:25:48.953][private$bdb$getRequestScheduler()$re ...] Register connector nci.cactus.
biodb.DEBUG[2024-06-29 16:25:48.954][private$addConnectorRules] Create new rule for URL "cactus.nci.nih.gov" of connector "nci.cactus".
biodb.DEBUG[2024-06-29 16:25:48.955][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-29 16:25:48.956][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-06-29 16:25:48.957][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-29 16:25:48.958][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-29 16:25:48.959][rule$addConnector] Connector "nci.cactus" is already listed in rule "cactus.nci.nih.gov".
biodb.DEBUG[2024-06-29 16:25:48.960][biodb$getFactory()$createConn] Creating new connector nci.cactus for database class nci.cactus .
biodb.INFO [2024-06-29 16:25:48.960][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-06-29 16:25:48.961][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector nci.cactus from the request scheduler
biodb.INFO [2024-06-29 16:25:48.962][self$deleteConn] Connector "nci.cactus" deleted.
biodb.DEBUG[2024-06-29 16:25:48.963][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-06-29 16:25:48.963][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-06-29 16:25:48.964][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-06-29 16:25:48.965][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-06-29 16:25:48.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-06-29 16:25:48.966][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-06-29 16:25:48.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ]
>
> proc.time()
user system elapsed
1007.511 206.465 1371.515
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbNci_1.9.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck’
* using R version 4.4.1 RC (2024-06-06 r86719)
* 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 ‘biodbNci/DESCRIPTION’ ... OK
* this is package ‘biodbNci’ version ‘1.9.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbNci’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
Running ‘testthat.R’
OK
* DONE
Status: OK
biodbNci.Rcheck/00install.out
* installing *source* package ‘biodbNci’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c extractEntries.cpp -o extractEntries.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c test-100-example.cpp -o test-100-example.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/testthat/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c test-runner.cpp -o test-runner.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o biodbNci.so RcppExports.o extractEntries.o test-100-example.o test-runner.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc-longtests/meat/biodbNci.Rcheck/00LOCK-biodbNci/00new/biodbNci/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbNci)