Package: TSRchitect

Version: 1.9.0

Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/TSRchitect_1.9.0.tar.gz && rm -rf TSRchitect.buildbin-libdir && mkdir TSRchitect.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TSRchitect.buildbin-libdir TSRchitect_1.9.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL TSRchitect_1.9.0.zip && rm TSRchitect_1.9.0.tar.gz TSRchitect_1.9.0.zip

StartedAt: 2019-04-08 20:06:54 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 20:08:48 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 114.3 seconds

RetCode: 0

Status:  OK

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### Running command:
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###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/TSRchitect_1.9.0.tar.gz && rm -rf TSRchitect.buildbin-libdir && mkdir TSRchitect.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TSRchitect.buildbin-libdir TSRchitect_1.9.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL TSRchitect_1.9.0.zip && rm TSRchitect_1.9.0.tar.gz TSRchitect_1.9.0.zip
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install for i386

* installing *source* package 'TSRchitect' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'TSRchitect'
    finding HTML links ... done
    TSRchitectUsersGuide                    html  
    addAnnotationToTSR-methods              html  
    finding level-2 HTML links ... done

    addTagCountsToTSR-methods               html  
    bedToTSS-methods                        html  
    cDNAtoBED-methods                       html  
    createSummarizedExperiment-methods      html  
    detTSR-methods                          html  
    determineTSR-methods                    html  
    getBamData-methods                      html  
    getFileNames-methods                    html  
    getTSRdata-methods                      html  
    getTSScountData-methods                 html  
    getTSStagData-methods                   html  
    getTitle-methods                        html  
    importAnnotationExternal-methods        html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpKAGBpz/R.INSTALL1ca87ba237da/TSRchitect/man/importAnnotationExternal-methods.Rd:37: file link 'import.bed' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpKAGBpz/R.INSTALL1ca87ba237da/TSRchitect/man/importAnnotationExternal-methods.Rd:38: file link 'import.gff' in package 'rtracklayer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpKAGBpz/R.INSTALL1ca87ba237da/TSRchitect/man/importAnnotationExternal-methods.Rd:39: file link 'import.gff3' in package 'rtracklayer' does not exist and so has been treated as a topic
    importAnnotationHub-methods             html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpKAGBpz/R.INSTALL1ca87ba237da/TSRchitect/man/importAnnotationHub-methods.Rd:44: file link 'AnnotationHub' in package 'AnnotationHub' does not exist and so has been treated as a topic
    inputToTSS-methods                      html  
    loadTSSobj-methods                      html  
    makeGRangesFromTSR-methods              html  
    mergeSampleData-methods                 html  
    processTSS-methods                      html  
    tsrCluster                              html  
    tssObject                               html  
    writeTSR-methods                        html  
** building package indices
** installing vignettes
   'TSRchitect.Rmd' using 'UTF-8' 
   'TSRchitectUsersGuide.Rmd' using 'UTF-8' 
Warning in res[i] <- withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),  :
  number of items to replace is not a multiple of replacement length
Warning in res[i] <- withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),  :
  number of items to replace is not a multiple of replacement length
Warning in res[i] <- withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),  :
  number of items to replace is not a multiple of replacement length
** 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 'TSRchitect' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TSRchitect' as TSRchitect_1.9.0.zip
* DONE (TSRchitect)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'TSRchitect' successfully unpacked and MD5 sums checked