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BUILD BIN report for h5vc on tokay2

This page was generated on 2019-10-16 12:28:53 -0400 (Wed, 16 Oct 2019).

Package 739/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
h5vc 2.18.0
Paul Theodor Pyl
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/h5vc
Branch: RELEASE_3_9
Last Commit: 8ec7cd5
Last Changed Date: 2019-05-02 11:53:46 -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  WARNINGS [ 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: h5vc
Version: 2.18.0
Command: rm -rf h5vc.buildbin-libdir && mkdir h5vc.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=h5vc.buildbin-libdir h5vc_2.18.0.tar.gz
StartedAt: 2019-10-16 09:24:40 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 09:26:00 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 80.3 seconds
RetCode: 0
Status:  OK  
PackageFile: h5vc_2.18.0.zip
PackageFileSize: 1.954 MiB

Command output

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###
### Running command:
###
###   rm -rf h5vc.buildbin-libdir && mkdir h5vc.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=h5vc.buildbin-libdir h5vc_2.18.0.tar.gz
###
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install for i386

* installing *source* package 'h5vc' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c bam.c -o bam.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c bam_plbuf.c -o bam_plbuf.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c sam.c -o sam.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c tallyBAM.cpp -o tallyBAM.o
tallyBAM.cpp: In function 'int pileup_func_old(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)':
tallyBAM.cpp:47:7: warning: unused variable 'len' [-Wunused-variable]
   int len = nttable->end - nttable->beg;
       ^
tallyBAM.cpp: In function 'int pileup_func(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)':
tallyBAM.cpp:96:7: warning: unused variable 'len' [-Wunused-variable]
   int len = nttable->end - nttable->beg;
       ^
tallyBAM.cpp: In function 'int _tallyBAM(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*)':
tallyBAM.cpp:140:6: warning: unused variable 'c' [-Wunused-variable]
  int c = 0;
      ^
tallyBAM.cpp: At global scope:
tallyBAM.cpp:43:12: warning: 'int pileup_func_old(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)' defined but not used [-Wunused-function]
 static int pileup_func_old(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data)
            ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o h5vc.dll tmp.def bam.o bam_plbuf.o sam.o tallyBAM.o -LC:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/usrlib/i386 -lhts -lz -lm -lws2_32 -lpthread -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/h5vc.buildbin-libdir/00LOCK-h5vc/00new/h5vc/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'h5vc'
    finding HTML links ... done
    applyTallies                            html  
    batchTallies                            html  
    binGenome                               html  
    binnedAFs                               html  
    callVariants                            html  
    callVariantsFisher                      html  
    callVariantsSingle                      html  
    coverage                                html  
    geom_h5vc                               html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpkJZFDN/R.INSTALL2e88523a66d/h5vc/man/geom_h5vc.Rd:25: file link 'geom_rect' in package 'ggplot2' does not exist and so has been treated as a topic
    getSampleData                           html  
    h5dapply                                html  
    h5readBlock                             html  
    h5vc-package                            html  
    helpers                                 html  
    mergeTallies                            html  
    mergeTallyFiles                         html  
    mismatchPlot                            html  
    mutationSpectrum                        html  
    plotMutationSpectrum                    html  
    prepareForHDF5                          html  
    prepareTallyFile                        html  
    tallyBAM                                html  
    tallyRanges                             html  
    finding level-2 HTML links ... done

    writeReference                          html  
    writeToTallyFile                        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 'h5vc' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c bam.c -o bam.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c bam_plbuf.c -o bam_plbuf.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c sam.c -o sam.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c tallyBAM.cpp -o tallyBAM.o
tallyBAM.cpp: In function 'int pileup_func_old(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)':
tallyBAM.cpp:47:7: warning: unused variable 'len' [-Wunused-variable]
   int len = nttable->end - nttable->beg;
       ^
tallyBAM.cpp: In function 'int pileup_func(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)':
tallyBAM.cpp:96:7: warning: unused variable 'len' [-Wunused-variable]
   int len = nttable->end - nttable->beg;
       ^
tallyBAM.cpp: In function 'int _tallyBAM(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*)':
tallyBAM.cpp:140:6: warning: unused variable 'c' [-Wunused-variable]
  int c = 0;
      ^
tallyBAM.cpp: At global scope:
tallyBAM.cpp:43:12: warning: 'int pileup_func_old(uint32_t, uint32_t, int, const bam_pileup1_t*, void*)' defined but not used [-Wunused-function]
 static int pileup_func_old(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data)
            ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o h5vc.dll tmp.def bam.o bam_plbuf.o sam.o tallyBAM.o -LC:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/usrlib/x64 -lhts -lz -lm -lws2_32 -lpthread -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/h5vc.buildbin-libdir/h5vc/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'h5vc' as h5vc_2.18.0.zip
* DONE (h5vc)