Back to Multiple platform build/check report for BioC 3.18:   simplified   long
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

This page was generated on 2023-10-02 11:39:14 -0400 (Mon, 02 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4660
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4396
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4416
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4401
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 1492/2233HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
paxtoolsr 1.35.0  (landing page)
Augustin Luna
Snapshot Date: 2023-10-01 14:05:07 -0400 (Sun, 01 Oct 2023)
git_url: https://git.bioconductor.org/packages/paxtoolsr
git_branch: devel
git_last_commit: 059017a
git_last_commit_date: 2023-04-25 10:35:26 -0400 (Tue, 25 Apr 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

CHECK results for paxtoolsr on lconway


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: 1.35.0
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_1.35.0.tar.gz
StartedAt: 2023-10-01 22:47:40 -0400 (Sun, 01 Oct 2023)
EndedAt: 2023-10-01 22:50:24 -0400 (Sun, 01 Oct 2023)
EllapsedTime: 164.6 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_1.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/paxtoolsr.Rcheck’
* using R version 4.3.1 Patched (2023-06-17 r84564)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘paxtoolsr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘paxtoolsr’ version ‘1.35.0’
* 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 R 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 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: 80 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 0 | SKIP 10 | PASS 39 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-3.18-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/4.3-x86_64/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 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

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 
2023-10-01 22:49:56,988 556  [main] INFO  org.biopax.paxtools.PaxtoolsMain  - Collecting proteins for a pathway, the converter will also consider its sub-pathways, their sub-pathways, etc.
2023-10-01 22:49:56,999 567  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - Begin converting Glycolysis Pathway pathway, uri=http://www.biopax.org/examples/myExamplePathway50
2023-10-01 22:49:57,005 573  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - - fetched PRs: 2
2023-10-01 22:49:57,005 573  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - - grouping the PRs by organism...
2023-10-01 22:49:57,015 583  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - - creating GSEA/GMT entries...
2023-10-01 22:49:57,016 584  [pool-2-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - adding uniprot IDs of  proteins (PRs) from 'Glycolysis Pathway', amaze;kegg pathway...
2023-10-01 22:49:57,018 586  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - - collected 1entries.
2023-10-01 22:49:57,018 586  [main] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - Creating entries for the rest fo (unused) PRs...
2023-10-01 22:50:02,340 5908 [main] INFO  org.biopax.paxtools.client.BiopaxValidatorClient  - BioPAX Validator location: http://biopax.baderlab.org/check.html
2023-10-01 22:50:10,175 13743 [main] INFO  org.biopax.paxtools.client.BiopaxValidatorClient  - BioPAX Validator location: http://biopax.baderlab.org/check.html
2023-10-01 22:50:11,197 14765 [main] INFO  org.biopax.paxtools.PaxtoolsMain  - Elements in the result model: 240
SBGN-PD Layout is running...
success ratio: 0.7857142857142857
enhanced ratio: 0.7857142857142857
Total execution time: 75 miliseconds.
2023-10-01 22:50:11,748 15316 [main] INFO  org.biopax.paxtools.PaxtoolsMain  - toSifnx: not blacklisting ubiquitous molecules (no blacklist.txt found)
2023-10-01 22:50:12,485 16053 [main] INFO  org.biopax.paxtools.PaxtoolsMain  - toSif: not blacklisting ubiquitous molecules (no blacklist.txt found)
2023-10-01 22:50:13,103 16671 [main] INFO  org.biopax.paxtools.PaxtoolsMain  - toSif: not blacklisting ubiquitous molecules (no blacklist.txt found)
[ FAIL 1 | WARN 0 | 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 0 | SKIP 10 | PASS 39 ]
Error: Test failures
Execution halted

Example timings

paxtoolsr.Rcheck/paxtoolsr-Ex.timings

nameusersystemelapsed
addAttributeList0.0210.0030.025
convertDataFrameListsToVectors0.0030.0000.003
convertSifToGmt0.1980.0340.277
downloadFile0.0350.0116.693
downloadPc20.0000.0010.000
downloadSignedPC000
fetch3.2380.3792.587
filterSif0.2890.0360.108
getCacheFiles000
getErrorMessage0.0020.0010.001
getNeighbors0.5970.0480.105
getPc0.0010.0000.000
getPcDatabaseNames0.2250.0090.339
getPcUrl000
getShortestPathSif0.0330.0020.037
getSifInteractionCategories0.0010.0000.000
graphPc0.0630.0000.064
integrateBiopax2.1790.2440.553
loadSifInIgraph0.0180.0010.009
mapValues0.0000.0000.001
mergeBiopax0.6640.0820.359
pcDirections0.0010.0000.001
pcFormats0.0000.0000.001
pcGraphQueries000
processPcRequest0.0050.0020.007
readBiopax0.0020.0000.005
readGmt0.0220.0030.025
readPcPathwaysInfo48.379 9.73860.146
readSbgn0.0020.0010.033
readSif0.0110.0010.019
readSifnx0.0190.0060.049
searchListOfVectors0.0010.0010.002
searchPc000
summarize0.0850.0130.086
summarizeSif0.0350.0020.013
toCytoscape0.0500.0080.027
toGSEA0.0770.0200.049
toLevel30.1160.0200.048