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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:paxtoolsr.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings paxtoolsr_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/paxtoolsr.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.22.0'
* 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 whether package 'paxtoolsr' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 31.8Mb
  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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
readPcPathwaysInfo 64.16   0.31   66.31
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
readPcPathwaysInfo 53.53   0.16   53.69
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/paxtoolsr.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/paxtoolsr_1.22.0.tar.gz && rm -rf paxtoolsr.buildbin-libdir && mkdir paxtoolsr.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=paxtoolsr.buildbin-libdir paxtoolsr_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL paxtoolsr_1.22.0.zip && rm paxtoolsr_1.22.0.tar.gz paxtoolsr_1.22.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 24.2M  100 24.2M    0     0  53.8M      0 --:--:-- --:--:-- --:--:-- 54.7M

install for i386

* 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

install for x64

* installing *source* package 'paxtoolsr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'paxtoolsr' as paxtoolsr_1.22.0.zip
* DONE (paxtoolsr)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'paxtoolsr' successfully unpacked and MD5 sums checked