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This page was generated on 2021-10-15 15:06:15 -0400 (Fri, 15 Oct 2021).

CHECK results for paxtoolsr on tokay2

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raw results

Package 1355/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
paxtoolsr 1.26.0  (landing page)
Augustin Luna
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/paxtoolsr
git_branch: RELEASE_3_13
git_last_commit: 7635a83
git_last_commit_date: 2021-05-19 12:08:34 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: paxtoolsr
Version: 1.26.0
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:paxtoolsr.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings paxtoolsr_1.26.0.tar.gz
StartedAt: 2021-10-15 03:12:36 -0400 (Fri, 15 Oct 2021)
EndedAt: 2021-10-15 03:14:52 -0400 (Fri, 15 Oct 2021)
EllapsedTime: 136.5 seconds
RetCode: 0
Status:   OK  
CheckDir: paxtoolsr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:paxtoolsr.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings paxtoolsr_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/paxtoolsr.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'paxtoolsr/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'paxtoolsr' version '1.26.0'
* 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 whether package 'paxtoolsr' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 31.9Mb
  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 34.33   0.13   34.48
fetch               5.58   0.37    2.40
validate            1.97   0.20    7.03
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/paxtoolsr.Rcheck/00check.log'
for details.



Installation output

paxtoolsr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch paxtoolsr
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
* installing *source* package 'paxtoolsr' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'paxtoolsr'
    finding HTML links ... done
    addAttributeList                        html  
    convertDataFrameListsToVectors          html  
    convertSifToGmt                         html  
    downloadFile                            html  
    downloadPc2                             html  
    downloadSignedPC                        html  
    fetch                                   html  
    filterSif                               html  
    getCacheFiles                           html  
    getErrorMessage                         html  
    getNeighbors                            html  
    getPc                                   html  
    getPcDatabaseNames                      html  
    getPcUrl                                html  
    getShortestPathSif                      html  
    getSifInteractionCategories             html  
    graphPc                                 html  
    integrateBiopax                         html  
    loadSifInIgraph                         html  
    mapAttributes                           html  
    mapValues                               html  
    mergeBiopax                             html  
    pcDirections                            html  
    pcFormats                               html  
    pcGraphQueries                          html  
    processPcRequest                        html  
    readBiopax                              html  
    readGmt                                 html  
    readPcPathwaysInfo                      html  
    readSbgn                                html  
    readSif                                 html  
    readSifnx                               html  
    searchListOfVectors                     html  
    searchPc                                html  
    splitSifnxByPathway                     html  
    summarize                               html  
    summarizeSif                            html  
    toCytoscape                             html  
    toGSEA                                  html  
    toLevel3                                html  
    toSBGN                                  html  
    toSif                                   html  
    toSifnx                                 html  
    topPathways                             html  
    traverse                                html  
    validate                                html  
** 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)
Making 'packages.html' ... done

Tests output

paxtoolsr.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 
2021-10-15 03:14:38,943 500  [main] INFO  org.biopax.paxtools.PaxtoolsMain  - Collecting proteins for a pathway, the converter will also consider its sub-pathways, their sub-pathways, etc.
2021-10-15 03:14:38,958 515  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - Begin converting Glycolysis Pathway pathway, uri=http://www.biopax.org/examples/myExamplePathway50
2021-10-15 03:14:38,958 515  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - - fetched PRs: 2
2021-10-15 03:14:38,958 515  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - - grouping the PRs by organism...
2021-10-15 03:14:38,974 531  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - - creating GSEA/GMT entries...
2021-10-15 03:14:38,974 531  [pool-2-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - adding uniprot IDs of  proteins (PRs) from 'Glycolysis Pathway', amaze;kegg pathway...
2021-10-15 03:14:38,974 531  [pool-1-thread-1] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - - collected 1entries.
2021-10-15 03:14:38,974 531  [main] INFO  org.biopax.paxtools.io.gsea.GSEAConverter  - Creating entries for the rest fo (unused) PRs...
2021-10-15 03:14:39,505 1062 [main] INFO  org.biopax.paxtools.client.BiopaxValidatorClient  - BioPAX Validator location: http://biopax.baderlab.org/check.html
2021-10-15 03:14:40,505 2062 [main] INFO  org.biopax.paxtools.client.BiopaxValidatorClient  - BioPAX Validator location: http://biopax.baderlab.org/check.html
2021-10-15 03:14:41,052 2609 [main] INFO  org.biopax.paxtools.PaxtoolsMain  - Elements in the result model: 240
SBGN-PD Layout is running...
success ratio: 0.8571428571428571
enhanced ratio: 0.8571428571428571
Total execution time: 172 miliseconds.
2021-10-15 03:14:41,833 3390 [main] INFO  org.biopax.paxtools.PaxtoolsMain  - toSifnx: not blacklisting ubiquitous molecules (no blacklist.txt found)
2021-10-15 03:14:43,630 5187 [main] INFO  org.biopax.paxtools.PaxtoolsMain  - toSif: not blacklisting ubiquitous molecules (no blacklist.txt found)
2021-10-15 03:14:44,224 5781 [main] INFO  org.biopax.paxtools.PaxtoolsMain  - toSif: not blacklisting ubiquitous molecules (no blacklist.txt found)
== Skipped tests ===============================================================
* On Bioconductor (7)
* empty test (3)

[ FAIL 0 | WARN 0 | SKIP 10 | PASS 40 ]
> 
> proc.time()
   user  system elapsed 
  21.54    0.98   16.29 

Example timings

paxtoolsr.Rcheck/paxtoolsr-Ex.timings

nameusersystemelapsed
addAttributeList0.020.000.02
convertDataFrameListsToVectors0.020.000.01
convertSifToGmt0.290.030.33
downloadFile0.120.020.41
downloadPc2000
downloadSignedPC000
fetch5.580.372.40
filterSif0.580.030.44
getCacheFiles0.000.040.02
getErrorMessage000
getNeighbors1.250.090.59
getPc000
getPcDatabaseNames0.030.000.30
getPcUrl000
getShortestPathSif0.050.000.04
getSifInteractionCategories000
graphPc000
integrateBiopax3.760.171.02
loadSifInIgraph0.110.020.05
mapValues000
mergeBiopax1.410.010.48
pcDirections0.030.000.02
pcFormats000
pcGraphQueries000
processPcRequest0.050.000.04
readBiopax000
readGmt0.070.000.10
readPcPathwaysInfo34.33 0.1334.48
readSbgn0.000.000.02
readSif0.020.000.01
readSifnx0.010.010.25
searchListOfVectors000
searchPc000
summarize0.140.000.36
summarizeSif0.020.000.02
toCytoscape0.020.020.03
toGSEA0.250.000.14
toLevel30.530.030.13
toSBGN1.760.162.07
toSif2.700.200.81
toSifnx3.130.080.60
topPathways000
traverse000
validate1.970.207.03