Multiple platform build/check report for BioC 3.12 - CHECK report for paxtoolsr on merida1

Package: paxtoolsr

Version: 1.24.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:paxtoolsr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings paxtoolsr_1.24.0.tar.gz

StartedAt: 2021-05-06 04:33:18 -0400 (Thu, 06 May 2021)

EndedAt: 2021-05-06 04:35:45 -0400 (Thu, 06 May 2021)

EllapsedTime: 146.6 seconds

RetCode: 1

Status: ERROR

CheckDir: paxtoolsr.Rcheck

Warnings: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:paxtoolsr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings paxtoolsr_1.24.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/paxtoolsr.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘paxtoolsr/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘paxtoolsr’ version ‘1.24.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 31.6Mb
  sub-directories of 1Mb or more:
    extdata   6.9Mb
    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 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) 
No Java runtime present, requesting install.
2021-05-06 04:35:23.420 R[10247:213543943] JLRequestRuntimeInstall: Error calling: CFMessagePortCreateRemote
* 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_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 
  2021-05-06 04:35:34,686 781  [main] INFO  org.biopax.paxtools.PaxtoolsMain  - Collecting proteins for a pathway, the converter will also consider its sub-pathways, their sub-pathways, etc.
  2021-05-06 04:35:34,701 796  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - Begin converting Glycolysis Pathway pathway, uri=http://www.biopax.org/examples/myExamplePathway50
  2021-05-06 04:35:34,710 805  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - - fetched PRs: 2
  2021-05-06 04:35:34,710 805  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - - grouping the PRs by organism...
  2021-05-06 04:35:34,724 819  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - - creating GSEA/GMT entries...
  2021-05-06 04:35:34,725 820  [pool-2-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - adding uniprot IDs of  proteins (PRs) from 'Glycolysis Pathway', amaze;kegg pathway...
  2021-05-06 04:35:34,728 823  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - - collected 1entries.
  2021-05-06 04:35:34,729 824  [main] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - Creating entries for the rest fo (unused) PRs...
  2021-05-06 04:35:35,529 1624 [main] INFO  org.biopax.paxtools.client.BiopaxValidatorClient  - BioPAX Validator location: http://biopax.baderlab.org/check.html
  2021-05-06 04:35:36,265 2360 [main] INFO  org.biopax.paxtools.client.BiopaxValidatorClient  - BioPAX Validator location: http://biopax.baderlab.org/check.html
  2021-05-06 04:35:36,696 2791 [main] INFO  org.biopax.paxtools.PaxtoolsMain  - Elements in the result model: 240
  No Java runtime present, requesting install.
  2021-05-06 04:35:36.938 R[12641:213548114] JLRequestRuntimeInstall: Error calling: CFMessagePortCreateRemote
* 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/paxtoolsr.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL paxtoolsr
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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)


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
2021-05-06 04:35:34,686 781  [main] INFO  org.biopax.paxtools.PaxtoolsMain  - Collecting proteins for a pathway, the converter will also consider its sub-pathways, their sub-pathways, etc.
2021-05-06 04:35:34,701 796  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - Begin converting Glycolysis Pathway pathway, uri=http://www.biopax.org/examples/myExamplePathway50
2021-05-06 04:35:34,710 805  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - - fetched PRs: 2
2021-05-06 04:35:34,710 805  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - - grouping the PRs by organism...
2021-05-06 04:35:34,724 819  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - - creating GSEA/GMT entries...
2021-05-06 04:35:34,725 820  [pool-2-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - adding uniprot IDs of  proteins (PRs) from 'Glycolysis Pathway', amaze;kegg pathway...
2021-05-06 04:35:34,728 823  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - - collected 1entries.
2021-05-06 04:35:34,729 824  [main] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - Creating entries for the rest fo (unused) PRs...
2021-05-06 04:35:35,529 1624 [main] INFO  org.biopax.paxtools.client.BiopaxValidatorClient  - BioPAX Validator location: http://biopax.baderlab.org/check.html
2021-05-06 04:35:36,265 2360 [main] INFO  org.biopax.paxtools.client.BiopaxValidatorClient  - BioPAX Validator location: http://biopax.baderlab.org/check.html
2021-05-06 04:35:36,696 2791 [main] INFO  org.biopax.paxtools.PaxtoolsMain  - Elements in the result model: 240
No Java runtime present, requesting install.
2021-05-06 04:35:36.938 R[12641:213548114] JLRequestRuntimeInstall: Error calling: CFMessagePortCreateRemote

name	user	system	elapsed
addAttributeList	0.022	0.002	0.024
convertDataFrameListsToVectors	0.005	0.001	0.006
convertSifToGmt	0.016	0.010	0.030
downloadFile	5.570	0.495	6.168
downloadPc2	0.000	0.001	0.001
downloadSignedPC	0.000	0.001	0.000
fetch	5.704	0.349	1.350
filterSif	0.519	0.023	0.124
getCacheFiles	0.001	0.000	0.001
getErrorMessage	0.001	0.001	0.001
getNeighbors	1.278	0.057	0.207
getPc	0.002	0.001	0.000
getPcDatabaseNames	0.147	0.005	0.207
getPcUrl	0.000	0.001	0.001
getShortestPathSif	0.029	0.001	0.031
getSifInteractionCategories	0.000	0.000	0.001
graphPc	0.001	0.000	0.000
integrateBiopax	3.234	0.184	0.926
loadSifInIgraph	0.031	0.001	0.008
mapValues	0.000	0.000	0.001
mergeBiopax	1.692	0.128	0.701
pcDirections	0.009	0.000	0.001
pcFormats	0.001	0.000	0.001
pcGraphQueries	0.001	0.001	0.000
processPcRequest	0.013	0.002	0.008
readBiopax	0.002	0.001	0.003
readGmt	0.074	0.002	0.039
readPcPathwaysInfo	54.923	5.888	60.841
readSbgn	0.002	0.001	0.003
readSif	0.004	0.001	0.005
readSifnx	0.019	0.003	0.023
searchListOfVectors	0.002	0.001	0.003
searchPc	0.000	0.001	0.000
summarize	0.135	0.013	0.087
summarizeSif	0.020	0.001	0.008
toCytoscape	0.033	0.001	0.024
toGSEA	0.161	0.013	0.055
toLevel3	0.406	0.020	0.115

CHECK report for paxtoolsr on merida1

Summary

Command output

Installation output

Tests output

Example timings