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BUILD BIN report for snapCGH on tokay2

This page was generated on 2019-10-16 12:20:23 -0400 (Wed, 16 Oct 2019).

Package 1547/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
snapCGH 1.54.0
John Marioni
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/snapCGH
Branch: RELEASE_3_9
Last Commit: 41a38a1
Last Changed Date: 2019-05-02 11:53:05 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: snapCGH
Version: 1.54.0
Command: rm -rf snapCGH.buildbin-libdir && mkdir snapCGH.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=snapCGH.buildbin-libdir snapCGH_1.54.0.tar.gz
StartedAt: 2019-10-16 10:15:25 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 10:16:00 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 35.3 seconds
RetCode: 0
Status:  OK  
PackageFile: snapCGH_1.54.0.zip
PackageFileSize: 1.217 MiB

Command output

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###
### Running command:
###
###   rm -rf snapCGH.buildbin-libdir && mkdir snapCGH.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=snapCGH.buildbin-libdir snapCGH_1.54.0.tar.gz
###
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install for i386

* installing *source* package 'snapCGH' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c optimizer.c -o optimizer.o
optimizer.c: In function 'fr_two':
optimizer.c:26:30: warning: unused variable 'temp3' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                              ^
optimizer.c:26:23: warning: unused variable 'temp2' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                       ^
optimizer.c:26:10: warning: unused variable 'denom' [-Wunused-variable]
   double denom, temp, temp2, temp3;
          ^
optimizer.c: In function 'fr_three':
optimizer.c:195:30: warning: unused variable 'temp3' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                              ^
optimizer.c:195:23: warning: unused variable 'temp2' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                       ^
optimizer.c:195:10: warning: unused variable 'denom' [-Wunused-variable]
   double denom, temp, temp2, temp3;
          ^
optimizer.c:194:69: warning: unused variable 'alphahat' [-Wunused-variable]
   double gammaA[3][3], gammaB[3][3], gammaC[3][3], alpha[3][nrow1], alphahat[3][nrow1], emis_prob[3][nrow1];
                                                                     ^
optimizer.c: In function 'fr_four':
optimizer.c:413:30: warning: unused variable 'temp3' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                              ^
optimizer.c:413:23: warning: unused variable 'temp2' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                       ^
optimizer.c:413:10: warning: unused variable 'denom' [-Wunused-variable]
   double denom, temp, temp2, temp3;
          ^
optimizer.c:412:69: warning: unused variable 'alphahat' [-Wunused-variable]
   double gammaA[4][4], gammaB[4][4], gammaC[4][4], alpha[4][nrow1], alphahat[4][nrow1], emis_prob[4][nrow1];
                                                                     ^
optimizer.c: In function 'fr_five':
optimizer.c:687:30: warning: unused variable 'temp3' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                              ^
optimizer.c:687:23: warning: unused variable 'temp2' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                       ^
optimizer.c:687:10: warning: unused variable 'denom' [-Wunused-variable]
   double denom, temp, temp2, temp3;
          ^
optimizer.c:686:69: warning: unused variable 'alphahat' [-Wunused-variable]
   double gammaA[5][5], gammaB[5][5], gammaC[5][5], alpha[5][nrow1], alphahat[5][nrow1], emis_prob[5][nrow1];
                                                                     ^
optimizer.c: In function 'fr_two':
optimizer.c:150:58: warning: 'gammaC[1][1]' may be used uninitialized in this function [-Wmaybe-uninitialized]
                 alpha[k][t] = alpha[k][t] + alpha[d][t-1]*gammaC[d][k];
                                                          ^
optimizer.c:150:58: warning: 'gammaC[1][0]' may be used uninitialized in this function [-Wmaybe-uninitialized]
optimizer.c:150:58: warning: 'gammaC[0][1]' may be used uninitialized in this function [-Wmaybe-uninitialized]
optimizer.c:150:58: warning: 'gammaC[0][0]' may be used uninitialized in this function [-Wmaybe-uninitialized]
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o snapCGH.dll tmp.def optimizer.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/snapCGH.buildbin-libdir/00LOCK-snapCGH/00new/snapCGH/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: more than one default provided in switch() call 
** help
*** installing help indices
  converting help for package 'snapCGH'
    finding HTML links ... done
    IDProbes                                html  
    LargeDataObject                         html  
    SegList                                 html  
    Viterbi.five                            html  
    Viterbi.four                            html  
    Viterbi.three                           html  
    Viterbi.two                             html  
    cbind                                   html  
    chrominfo.Mb                            html  
    compareSegmentations                    html  
    convert.output                          html  
    dim                                     html  
    dimnames                                html  
    filter                                  html  
    find.param.five                         html  
    find.param.four                         html  
    find.param.one                          html  
    find.param.three                        html  
    find.param.two                          html  
    findBreakPoints                         html  
    fit.model                               html  
    genomePlot                              html  
    heatmapGenome                           html  
    imputeMissingValues                     html  
    log2ratios                              html  
    mergeStates                             html  
    non.zero.length.distr.non.tiled         html  
    non.zero.length.distr.tiled             html  
    plotSegmentedGenome                     html  
    processCGH                              html  
    read.clonesinfo                         html  
    readPositionalInfo                      html  
    removeByWeights                         html  
    runBioHMM                               html  
    runDNAcopy                              html  
    runGLAD                                 html  
    runHMM                                  html  
    runTilingArray                          html  
    sim.structure                           html  
    zero.length.distr.non.tiled             html  
    zero.length.distr.tiled                 html  
    zoomChromosome                          html  
    zoomGenome                              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 'snapCGH' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c optimizer.c -o optimizer.o
optimizer.c: In function 'fr_two':
optimizer.c:26:30: warning: unused variable 'temp3' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                              ^
optimizer.c:26:23: warning: unused variable 'temp2' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                       ^
optimizer.c:26:10: warning: unused variable 'denom' [-Wunused-variable]
   double denom, temp, temp2, temp3;
          ^
optimizer.c: In function 'fr_three':
optimizer.c:195:30: warning: unused variable 'temp3' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                              ^
optimizer.c:195:23: warning: unused variable 'temp2' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                       ^
optimizer.c:195:10: warning: unused variable 'denom' [-Wunused-variable]
   double denom, temp, temp2, temp3;
          ^
optimizer.c:194:69: warning: unused variable 'alphahat' [-Wunused-variable]
   double gammaA[3][3], gammaB[3][3], gammaC[3][3], alpha[3][nrow1], alphahat[3][nrow1], emis_prob[3][nrow1];
                                                                     ^
optimizer.c: In function 'fr_four':
optimizer.c:413:30: warning: unused variable 'temp3' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                              ^
optimizer.c:413:23: warning: unused variable 'temp2' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                       ^
optimizer.c:413:10: warning: unused variable 'denom' [-Wunused-variable]
   double denom, temp, temp2, temp3;
          ^
optimizer.c:412:69: warning: unused variable 'alphahat' [-Wunused-variable]
   double gammaA[4][4], gammaB[4][4], gammaC[4][4], alpha[4][nrow1], alphahat[4][nrow1], emis_prob[4][nrow1];
                                                                     ^
optimizer.c: In function 'fr_five':
optimizer.c:687:30: warning: unused variable 'temp3' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                              ^
optimizer.c:687:23: warning: unused variable 'temp2' [-Wunused-variable]
   double denom, temp, temp2, temp3;
                       ^
optimizer.c:687:10: warning: unused variable 'denom' [-Wunused-variable]
   double denom, temp, temp2, temp3;
          ^
optimizer.c:686:69: warning: unused variable 'alphahat' [-Wunused-variable]
   double gammaA[5][5], gammaB[5][5], gammaC[5][5], alpha[5][nrow1], alphahat[5][nrow1], emis_prob[5][nrow1];
                                                                     ^
optimizer.c:943:4: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false [-Wstrict-overflow]
    for(t = 1; t < nrow1; t++){
    ^
optimizer.c: In function 'fr_four':
optimizer.c:585:1: warning: assuming signed overflow does not occur when assuming that (X + c) < X is always false [-Wstrict-overflow]
 for(t = 1; t < nrow1; t++){  
 ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o snapCGH.dll tmp.def optimizer.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/snapCGH.buildbin-libdir/snapCGH/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'snapCGH' as snapCGH_1.54.0.zip
* DONE (snapCGH)