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This page was generated on 2024-03-29 11:37:06 -0400 (Fri, 29 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4669
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4404
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4427
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 1511/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
paxtoolsr 1.36.0  (landing page)
Augustin Luna
Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/paxtoolsr
git_branch: RELEASE_3_18
git_last_commit: efd04f2
git_last_commit_date: 2023-10-24 10:39:18 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for paxtoolsr on palomino4


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: 1.36.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:paxtoolsr.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings paxtoolsr_1.36.0.tar.gz
StartedAt: 2024-03-28 03:40:37 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 03:42:53 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 136.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: paxtoolsr.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:paxtoolsr.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings paxtoolsr_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/paxtoolsr.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'paxtoolsr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'paxtoolsr' version '1.36.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package '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: 1.0
enhanced ratio: 1.0
Total execution time: 31 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 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
  'F:/biocbuild/bbs-3.18-bioc/meat/paxtoolsr.Rcheck/00check.log'
for details.


Installation output

paxtoolsr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL paxtoolsr
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/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 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
2024-03-28 03:42:39,962 690  [main] INFO  org.biopax.paxtools.PaxtoolsMain  - Collecting proteins for a pathway, the converter will also consider its sub-pathways, their sub-pathways, etc.
2024-03-28 03:42:40,008 736  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - Begin converting Glycolysis Pathway pathway, uri=http://www.biopax.org/examples/myExamplePathway50
2024-03-28 03:42:40,008 736  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - - fetched PRs: 2
2024-03-28 03:42:40,008 736  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - - grouping the PRs by organism...
2024-03-28 03:42:40,071 799  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - - creating GSEA/GMT entries...
2024-03-28 03:42:40,071 799  [pool-2-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - adding uniprot IDs of  proteins (PRs) from 'Glycolysis Pathway', amaze;kegg pathway...
2024-03-28 03:42:40,071 799  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - - collected 1entries.
2024-03-28 03:42:40,071 799  [main] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - Creating entries for the rest fo (unused) PRs...
2024-03-28 03:42:40,825 1553 [main] INFO  org.biopax.paxtools.client.BiopaxValidatorClient  - BioPAX Validator location: http://biopax.baderlab.org/check.html
2024-03-28 03:42:41,263 1991 [main] INFO  org.biopax.paxtools.client.BiopaxValidatorClient  - BioPAX Validator location: http://biopax.baderlab.org/check.html
2024-03-28 03:42:41,732 2460 [main] INFO  org.biopax.paxtools.PaxtoolsMain  - Elements in the result model: 240
SBGN-PD Layout is running...
success ratio: 0.7857142857142857
enhanced ratio: 0.8571428571428571
Total execution time: 94 miliseconds.
2024-03-28 03:42:42,591 3319 [main] INFO  org.biopax.paxtools.PaxtoolsMain  - toSifnx: not blacklisting ubiquitous molecules (no blacklist.txt found)
2024-03-28 03:42:43,311 4039 [main] INFO  org.biopax.paxtools.PaxtoolsMain  - toSif: not blacklisting ubiquitous molecules (no blacklist.txt found)
2024-03-28 03:42:43,967 4695 [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
addAttributeList0.090.000.10
convertDataFrameListsToVectors000
convertSifToGmt0.390.050.83
downloadFile0.030.010.14
downloadPc2000
downloadSignedPC000
fetch3.410.321.13
filterSif0.840.010.23
getCacheFiles000
getErrorMessage0.050.000.02
getNeighbors0.860.060.22
getPc000
getPcDatabaseNames0.120.000.26
getPcUrl000
getShortestPathSif0.080.000.09
getSifInteractionCategories000
graphPc000
integrateBiopax2.440.160.68
loadSifInIgraph0.090.000.03
mapValues000
mergeBiopax1.130.060.48
pcDirections000
pcFormats000
pcGraphQueries000
processPcRequest0.000.000.03
readBiopax0.020.000.01
readGmt0.080.000.08
readPcPathwaysInfo51.42 2.9254.46
readSbgn000
readSif0.010.000.02
readSifnx0.030.000.06
searchListOfVectors000
searchPc000
summarize0.140.000.09
summarizeSif0.020.000.02
toCytoscape0.020.020.03
toGSEA0.120.030.06
toLevel30.200.020.07