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INSTALL report for TFBSTools on tokay1

This page was generated on 2020-04-15 12:22:19 -0400 (Wed, 15 Apr 2020).

Package 1717/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TFBSTools 1.24.0
Ge Tan
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/TFBSTools
Branch: RELEASE_3_10
Last Commit: 952afaa
Last Changed Date: 2019-10-29 13:08:50 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: TFBSTools
Version: 1.24.0
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/TFBSTools_1.24.0.tar.gz && rm -rf TFBSTools.buildbin-libdir && mkdir TFBSTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TFBSTools.buildbin-libdir TFBSTools_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL TFBSTools_1.24.0.zip && rm TFBSTools_1.24.0.tar.gz TFBSTools_1.24.0.zip
StartedAt: 2020-04-14 19:56:24 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 19:57:41 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 77.1 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/TFBSTools_1.24.0.tar.gz && rm -rf TFBSTools.buildbin-libdir && mkdir TFBSTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TFBSTools.buildbin-libdir TFBSTools_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL TFBSTools_1.24.0.zip && rm TFBSTools_1.24.0.tar.gz TFBSTools_1.24.0.zip
###
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100  150k  100  150k    0     0  2270k      0 --:--:-- --:--:-- --:--:-- 2394k

install for i386

* installing *source* package 'TFBSTools' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -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-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_TFBSTools.c -o R_init_TFBSTools.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o TFBSTools.dll tmp.def matrixAlignerDynamic.o R_init_TFBSTools.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/TFBSTools.buildbin-libdir/00LOCK-TFBSTools/00new/TFBSTools/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'IRanges' for request: 'score' when loading 'TFBSTools'
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  
    writeGFF3-methods                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package 'IRanges' for request: 'score' when loading 'TFBSTools'
** testing if installed package can be loaded from final location
No methods found in package 'IRanges' for request: 'score' when loading 'TFBSTools'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'TFBSTools' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -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-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_TFBSTools.c -o R_init_TFBSTools.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o TFBSTools.dll tmp.def matrixAlignerDynamic.o R_init_TFBSTools.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/TFBSTools.buildbin-libdir/TFBSTools/libs/x64
** testing if installed package can be loaded
No methods found in package 'IRanges' for request: 'score' when loading 'TFBSTools'
* MD5 sums
packaged installation of 'TFBSTools' as TFBSTools_1.24.0.zip
* DONE (TFBSTools)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'TFBSTools' successfully unpacked and MD5 sums checked