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This page was generated on 2024-06-11 15:43 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 1484/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
paxtoolsr 1.39.0  (landing page)
Augustin Luna
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/paxtoolsr
git_branch: devel
git_last_commit: 444550a
git_last_commit_date: 2024-04-30 10:39:35 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  skipped
palomino4Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
merida1macOS 12.7.4 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  


CHECK results for paxtoolsr on kjohnson1

To the developers/maintainers of the paxtoolsr package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/paxtoolsr.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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.

raw results


Summary

Package: paxtoolsr
Version: 1.39.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:paxtoolsr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings paxtoolsr_1.39.0.tar.gz
StartedAt: 2024-06-11 03:58:34 -0400 (Tue, 11 Jun 2024)
EndedAt: 2024-06-11 04:00:47 -0400 (Tue, 11 Jun 2024)
EllapsedTime: 132.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: paxtoolsr.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:paxtoolsr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings paxtoolsr_1.39.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/paxtoolsr.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-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 Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘paxtoolsr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘paxtoolsr’ version ‘1.39.0’
* 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 ‘paxtoolsr’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 32.1Mb
  sub-directories of 1Mb or more:
    extdata   7.3Mb
    java     24.5Mb
* checking package directory ... OK
* checking ‘build’ 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
splitSifnxByPathway: no visible global function definition for
  ‘%dopar%’
Undefined global functions or variables:
  %dopar%
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘paxtoolsr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: toSBGN
> ### Title: Convert a BioPAX OWL file to SBGNML
> ### Aliases: toSBGN
> 
> ### ** Examples
> 
> outFile <- tempfile()
> results <- toSBGN(system.file("extdata", "biopax3-short-metabolic-pathway.owl", 
+   package="paxtoolsr"), 
+   outFile) 
SBGN-PD Layout is running...
success ratio: 0.9285714285714286
enhanced ratio: 0.9285714285714286
Total execution time: 95 miliseconds.
Error in toSBGN(system.file("extdata", "biopax3-short-metabolic-pathway.owl",  : 
  java.lang.ExceptionInInitializerError
Calls: toSBGN -> .jcheck
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    'test_pathwayCommons.R:63:5', 'test_pathwayCommons.R:77:5',
    'test_pathwayCommons.R:131:5', 'test_pathwayCommons.R:169:5',
    'test_pathwayCommons.R:185:5', 'test_pathwayCommons.R:260:5'
  • empty test (3): 'test_pathwayCommons.R:266:1', 'test_pathwayCommons.R:285:1',
    'test_pathwayCommons.R:286:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_paxtools.R:73:5'): toSBGN ──────────────────────────────────────
  <ExceptionInInitializerError/LinkageError/Error/Throwable/Object/Exception/error/condition>
  Error in `toSBGN(system.file("extdata", "biopax3-short-metabolic-pathway.owl", 
      package = "paxtoolsr"), outFile)`: java.lang.ExceptionInInitializerError
  
  [ FAIL 1 | WARN 1 | SKIP 10 | PASS 39 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/paxtoolsr.Rcheck/00check.log’
for details.


Installation output

paxtoolsr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL paxtoolsr
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘paxtoolsr’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (paxtoolsr)

Tests output

paxtoolsr.Rcheck/tests/testthat.Rout.fail


R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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.

> library(testthat)
> library(paxtoolsr)
Loading required package: rJava
Loading required package: XML
Consider citing this package: Luna A, et al. PaxtoolsR: pathway analysis in R using Pathway Commons. PMID: 26685306; citation("paxtoolsr")
> 
> test_check("paxtoolsr")
URL:  http://www.pathwaycommons.org/pc2/get?uri=http%3A%2F%2Fidentifiers.org%2Funiprot%2FQ06609&uri=http%3A%2F%2Fidentifiers.org%2Funiprot%2FQ96EB6&format=BIOPAX 
2024-06-11 04:00:31,978 729  [main] INFO  org.biopax.paxtools.PaxtoolsMain  - Collecting proteins for a pathway, the converter will also consider its sub-pathways, their sub-pathways, etc.
2024-06-11 04:00:31,996 747  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - Begin converting Glycolysis Pathway pathway, uri=http://www.biopax.org/examples/myExamplePathway50
2024-06-11 04:00:32,003 754  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - - fetched PRs: 2
2024-06-11 04:00:32,004 755  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - - grouping the PRs by organism...
2024-06-11 04:00:32,013 764  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - - creating GSEA/GMT entries...
2024-06-11 04:00:32,015 766  [pool-2-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - adding uniprot IDs of  proteins (PRs) from 'Glycolysis Pathway', amaze;kegg pathway...
2024-06-11 04:00:32,019 770  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - - collected 1entries.
2024-06-11 04:00:32,020 771  [main] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - Creating entries for the rest fo (unused) PRs...
2024-06-11 04:00:32,764 1515 [main] INFO  org.biopax.paxtools.client.BiopaxValidatorClient  - BioPAX Validator location: http://biopax.baderlab.org/check.html
2024-06-11 04:00:33,943 2694 [main] INFO  org.biopax.paxtools.client.BiopaxValidatorClient  - BioPAX Validator location: http://biopax.baderlab.org/check.html
2024-06-11 04:00:34,560 3311 [main] INFO  org.biopax.paxtools.PaxtoolsMain  - Elements in the result model: 240
SBGN-PD Layout is running...
success ratio: 1.0
enhanced ratio: 1.0
Total execution time: 51 miliseconds.
2024-06-11 04:00:35,113 3864 [main] INFO  org.biopax.paxtools.PaxtoolsMain  - toSifnx: not blacklisting ubiquitous molecules (no blacklist.txt found)
2024-06-11 04:00:35,801 4552 [main] INFO  org.biopax.paxtools.PaxtoolsMain  - toSif: not blacklisting ubiquitous molecules (no blacklist.txt found)
2024-06-11 04:00:36,500 5251 [main] INFO  org.biopax.paxtools.PaxtoolsMain  - toSif: not blacklisting ubiquitous molecules (no blacklist.txt found)
[ FAIL 1 | WARN 1 | SKIP 10 | PASS 39 ]

══ Skipped tests (10) ══════════════════════════════════════════════════════════
• On Bioconductor (7): 'test_pathwayCommons.R:38:5',
  'test_pathwayCommons.R:63:5', 'test_pathwayCommons.R:77:5',
  'test_pathwayCommons.R:131:5', 'test_pathwayCommons.R:169:5',
  'test_pathwayCommons.R:185:5', 'test_pathwayCommons.R:260:5'
• empty test (3): 'test_pathwayCommons.R:266:1', 'test_pathwayCommons.R:285:1',
  'test_pathwayCommons.R:286:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_paxtools.R:73:5'): toSBGN ──────────────────────────────────────
<ExceptionInInitializerError/LinkageError/Error/Throwable/Object/Exception/error/condition>
Error in `toSBGN(system.file("extdata", "biopax3-short-metabolic-pathway.owl", 
    package = "paxtoolsr"), outFile)`: java.lang.ExceptionInInitializerError

[ FAIL 1 | WARN 1 | SKIP 10 | PASS 39 ]
Error: Test failures
Execution halted

Example timings

paxtoolsr.Rcheck/paxtoolsr-Ex.timings

nameusersystemelapsed
addAttributeList0.0960.0030.099
convertDataFrameListsToVectors0.0010.0000.001
convertSifToGmt0.2720.0250.301
downloadFile0.0360.0090.146
downloadPc2000
downloadSignedPC000
fetch3.1610.1711.215
filterSif0.2500.0190.234
getCacheFiles0.0000.0010.001
getErrorMessage0.0000.0000.001
getNeighbors0.4660.0220.143
getPc000
getPcDatabaseNames0.6190.0120.433
getPcUrl0.0030.0000.001
getShortestPathSif0.0490.0050.051
getSifInteractionCategories0.0010.0000.001
graphPc0.0000.0000.001
integrateBiopax2.4600.1210.778
loadSifInIgraph0.0400.0030.015
mapValues0.0010.0000.000
mergeBiopax1.2950.0810.518
pcDirections0.0010.0010.000
pcFormats000
pcGraphQueries0.0000.0010.000
processPcRequest0.0120.0020.008
readBiopax0.0040.0010.006
readGmt0.0210.0020.023
readPcPathwaysInfo48.762 5.85755.197
readSbgn0.0020.0010.005
readSif0.0090.0010.009
readSifnx0.0160.0070.022
searchListOfVectors0.0000.0000.001
searchPc000
summarize0.1280.0110.065
summarizeSif0.0270.0060.013
toCytoscape0.0540.0030.027
toGSEA0.1750.0190.078
toLevel30.2210.0130.078