Back to Multiple platform build/check report for BioC 3.11
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

CHECK report for paxtoolsr on malbec2

This page was generated on 2020-10-17 11:55:21 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE paxtoolsr PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1279/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
paxtoolsr 1.22.0
Augustin Luna
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/paxtoolsr
Branch: RELEASE_3_11
Last Commit: e4c4062
Last Changed Date: 2020-04-27 14:44:11 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  ERROR  OK 

Summary

Package: paxtoolsr
Version: 1.22.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:paxtoolsr.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings paxtoolsr_1.22.0.tar.gz
StartedAt: 2020-10-17 03:57:39 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:59:36 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 117.2 seconds
RetCode: 0
Status:  OK 
CheckDir: paxtoolsr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:paxtoolsr.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings paxtoolsr_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/paxtoolsr.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (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 ‘1.22.0’
* 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 31.7Mb
  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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
readPcPathwaysInfo 43.7  0.543   44.16
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/paxtoolsr.Rcheck/00check.log’
for details.



Installation output

paxtoolsr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL paxtoolsr
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-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


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
2020-10-17 03:59:28,112 682  [main] INFO  org.biopax.paxtools.PaxtoolsMain  - Collecting proteins for a pathway, the converter will also consider its sub-pathways, their sub-pathways, etc.
2020-10-17 03:59:28,121 691  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - Begin converting Glycolysis Pathway pathway, uri=http://www.biopax.org/examples/myExamplePathway50
2020-10-17 03:59:28,128 698  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - - fetched PRs: 2
2020-10-17 03:59:28,128 698  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - - grouping the PRs by organism...
2020-10-17 03:59:28,140 710  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - - creating GSEA/GMT entries...
2020-10-17 03:59:28,143 713  [pool-2-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - adding uniprot IDs of  proteins (PRs) from 'Glycolysis Pathway', amaze;kegg pathway...
2020-10-17 03:59:28,145 715  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - - collected 1entries.
2020-10-17 03:59:28,145 715  [main] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - Creating entries for the rest fo (unused) PRs...
2020-10-17 03:59:28,554 1124 [main] INFO  org.biopax.paxtools.client.BiopaxValidatorClient  - BioPAX Validator location: http://biopax.baderlab.org/check.html
2020-10-17 03:59:29,172 1742 [main] INFO  org.biopax.paxtools.client.BiopaxValidatorClient  - BioPAX Validator location: http://biopax.baderlab.org/check.html
2020-10-17 03:59:29,662 2232 [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: 98 miliseconds.
2020-10-17 03:59:30,307 2877 [main] INFO  org.biopax.paxtools.PaxtoolsMain  - toSifnx: not blacklisting ubiquitous molecules (no blacklist.txt found)
2020-10-17 03:59:30,951 3521 [main] INFO  org.biopax.paxtools.PaxtoolsMain  - toSif: not blacklisting ubiquitous molecules (no blacklist.txt found)
2020-10-17 03:59:31,530 4100 [main] INFO  org.biopax.paxtools.PaxtoolsMain  - toSif: not blacklisting ubiquitous molecules (no blacklist.txt found)
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 40 | SKIPPED: 10 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 19.434   0.502  14.188 

Example timings

paxtoolsr.Rcheck/paxtoolsr-Ex.timings

nameusersystemelapsed
addAttributeList0.0350.0000.034
convertDataFrameListsToVectors0.0060.0000.007
convertSifToGmt0.0300.0080.048
downloadFile0.0930.0040.268
downloadPc2000
downloadSignedPC000
fetch3.6530.1471.071
filterSif0.2380.0000.080
getCacheFiles0.0010.0000.001
getErrorMessage0.0000.0000.001
getNeighbors0.8270.0070.184
getPc0.0000.0000.001
getPcDatabaseNames0.2440.0000.221
getPcUrl000
getShortestPathSif0.0880.0000.045
getSifInteractionCategories0.0010.0000.000
graphPc000
integrateBiopax3.1180.0710.753
loadSifInIgraph0.0120.0000.005
mapValues0.0010.0000.000
mergeBiopax1.0520.0240.390
pcDirections0.0000.0000.001
pcFormats000
pcGraphQueries000
processPcRequest0.0080.0000.003
readBiopax0.0060.0000.001
readGmt0.0430.0040.023
readPcPathwaysInfo43.700 0.54344.160
readSbgn0.0010.0000.002
readSif0.0020.0000.002
readSifnx0.0120.0000.012
searchListOfVectors0.0010.0000.001
searchPc000
summarize0.1560.0050.067
summarizeSif0.0040.0000.005
toCytoscape0.0190.0000.020
toGSEA0.1490.0000.071
toLevel30.3440.0040.066
toSBGN1.3530.0370.533
toSif2.4050.0270.491
toSifnx2.9120.0390.545
topPathways0.0010.0000.000
traverse000
validate1.5490.0611.205