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INSTALL report for TFBSTools on tokay1

This page was generated on 2018-04-12 13:23:31 -0400 (Thu, 12 Apr 2018).

Package 1395/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TFBSTools 1.16.0
Ge Tan
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/TFBSTools
Branch: RELEASE_3_6
Last Commit: 565436a
Last Changed Date: 2017-10-30 12:40:09 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TFBSTools
Version: 1.16.0
Command: rm -rf TFBSTools.buildbin-libdir && mkdir TFBSTools.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/TFBSTools_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=TFBSTools.buildbin-libdir --merge-multiarch TFBSTools_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL TFBSTools_1.16.0.zip && rm TFBSTools_1.16.0.tar.gz TFBSTools_1.16.0.zip
StartedAt: 2018-04-11 18:50:07 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 18:52:07 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 119.7 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   rm -rf TFBSTools.buildbin-libdir && mkdir TFBSTools.buildbin-libdir  && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/TFBSTools_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=TFBSTools.buildbin-libdir --merge-multiarch TFBSTools_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL TFBSTools_1.16.0.zip  && rm TFBSTools_1.16.0.tar.gz TFBSTools_1.16.0.zip
###
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install for i386

* installing *source* package 'TFBSTools' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c matrixAlignerDynamic.c -o matrixAlignerDynamic.o
matrixAlignerDynamic.c: In function 'score':
matrixAlignerDynamic.c:235:22: warning: 'best_pntr' may be used uninitialized in this function [-Wmaybe-uninitialized]
   while (current_pntr->father != NULL){ // while the father of the current pointer exists, walk through the best posible alignment
                      ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c R_init_TFBSTools.c -o R_init_TFBSTools.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o TFBSTools.dll tmp.def matrixAlignerDynamic.o R_init_TFBSTools.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/TFBSTools.buildbin-libdir/TFBSTools/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a new generic function for 'seqLogo' in package 'TFBSTools'
** help
*** installing help indices
  converting help for package 'TFBSTools'
    finding HTML links ... done
    IUPAC2Matrix                            html  
    MA0004.1                                html  
    MotifSet-class                          html  
    PFMSimilarity-methods                   html  
    PWMSimilarity-methods                   html  
    SitePairSet-class                       html  
    SitePairSetList-class                   html  
    SiteSet-class                           html  
    SiteSetList-class                       html  
    TFBSTools-package                       html  
    TFFM-class                              html  
    XMatrix-class                           html  
    XMatrixList-class                       html  
    calConservation-methods                 html  
    deleteMatrixHavingID-methods            html  
    dmmEM-methods                           html  
    getEmissionProb                         html  
    getMatrixByID-methods                   html  
    getMatrixSet-methods                    html  
    getPosProb                              html  
    makeFlatFileDir                         html  
    parseMEMEOutput                         html  
    permuteMatrix-methods                   html  
    rPWMDmm-methods                         html  
    readJASPARMatrix                        html  
    readXMLTFFM                             html  
    runMEME-methods                         html  
    sampleRanges                            html  
    searchAln-methods                       html  
    searchPairBSgenome-methods              html  
    searchSeq-methods                       html  
    seqLogo                                 html  
    shannon.entropy                         html  
    toGRangesList-methods                   html  
    toICM-methods                           html  
    finding level-2 HTML links ... done

    toPWM-methods                           html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp08MMit/R.INSTALL16447a1e21d/TFBSTools/man/toPWM-methods.Rd:91: missing file link 'PWM'
    writeGFF3-methods                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'TFBSTools' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c matrixAlignerDynamic.c -o matrixAlignerDynamic.o
matrixAlignerDynamic.c: In function 'score':
matrixAlignerDynamic.c:235:22: warning: 'best_pntr' may be used uninitialized in this function [-Wmaybe-uninitialized]
   while (current_pntr->father != NULL){ // while the father of the current pointer exists, walk through the best posible alignment
                      ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c R_init_TFBSTools.c -o R_init_TFBSTools.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o TFBSTools.dll tmp.def matrixAlignerDynamic.o R_init_TFBSTools.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/TFBSTools.buildbin-libdir/TFBSTools/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TFBSTools' as TFBSTools_1.16.0.zip
* DONE (TFBSTools)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.6-bioc/R/library'
package 'TFBSTools' successfully unpacked and MD5 sums checked
In R CMD INSTALL