##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/biovizBase_1.40.0.tar.gz && rm -rf biovizBase.buildbin-libdir && mkdir biovizBase.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=biovizBase.buildbin-libdir biovizBase_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL biovizBase_1.40.0.zip && rm biovizBase_1.40.0.tar.gz biovizBase_1.40.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  5 2135k    5  126k    0     0   531k      0  0:00:04 --:--:--  0:00:04  531k
 68 2135k   68 1457k    0     0  1187k      0  0:00:01  0:00:01 --:--:-- 1187k
100 2135k  100 2135k    0     0  1397k      0  0:00:01  0:00:01 --:--:-- 1396k

install for i386

* installing *source* package 'biovizBase' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_init_biovizBase.c -o R_init_biovizBase.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c bin_offsets.c -o bin_offsets.o
bin_offsets.c: In function 'scan_bam_bin_offsets':
bin_offsets.c:57:15: warning: pointer targets in passing argument 1 of 'strncmp' differ in signedness [-Wpointer-sign]
   if (strncmp(b, "BAI\1", 4))
               ^
In file included from C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/R_ext/RS.h:34,
                 from C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rdefines.h:39,
                 from bin_offsets.h:1,
                 from bin_offsets.c:3:
C:/rtools40/mingw32/i686-w64-mingw32/include/string.h:86:15: note: expected 'const char *' but argument is of type 'Rbyte *' {aka 'unsigned char *'}
   int __cdecl strncmp(const char *_Str1,const char *_Str2,size_t _MaxCount);
               ^~~~~~~
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o biovizBase.dll tmp.def R_init_biovizBase.o bin_offsets.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/biovizBase.buildbin-libdir/00LOCK-biovizBase/00new/biovizBase/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'biovizBase'
    finding HTML links ... done
    CRC                                     html  
    GCcontent                               html  
    addStepping-method                      html  
    aes-utils                               html  
    biovizBase-package                      html  
    colorBlindSafePal                       html  
    containLetters                          html  
    crc1.GeRL                               html  
    crunch-method                           html  
    darned_hg19_subset500                   html  
    estimateCoverage-method                 html  
    flatGrl                                 html  
    genesymbol                              html  
    getBioColor                             html  
    getFormalNames                          html  
    getGaps                                 html  
    getIdeoGR                               html  
    getIdeogram                             html  
    getScale                                html  
    hg19Ideogram                            html  
    hg19IdeogramCyto                        html  
    ideo                                    html  
    ideoCyto                                html  
    isIdeogram                              html  
    isMatchedWithModel                      html  
    isSimpleIdeogram                        html  
    labs                                    html  
    maxGap-method                           html  
    mold-method                             html  
    finding level-2 HTML links ... done

    pileupAsGRanges                         html  
    pileupGRangesAsVariantTable             html  
    plotColorLegend                         html  
    scale                                   html  
    showColor                               html  
    shrinkageFun-method                     html  
    splitByFacets-method                    html  
    strip_formula_dots                      html  
    subsetArgsByFormals                     html  
    transform                               html  
    transformGRangesForEvenSpace            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 'biovizBase' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c R_init_biovizBase.c -o R_init_biovizBase.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c bin_offsets.c -o bin_offsets.o
bin_offsets.c: In function 'scan_bam_bin_offsets':
bin_offsets.c:57:15: warning: pointer targets in passing argument 1 of 'strncmp' differ in signedness [-Wpointer-sign]
   if (strncmp(b, "BAI\1", 4))
               ^
In file included from C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/R_ext/RS.h:34,
                 from C:/Users/BIOCBU~1/BBS-3~1.13-/R/include/Rdefines.h:39,
                 from bin_offsets.h:1,
                 from bin_offsets.c:3:
C:/rtools40/mingw64/x86_64-w64-mingw32/include/string.h:86:15: note: expected 'const char *' but argument is of type 'Rbyte *' {aka 'unsigned char *'}
   int __cdecl strncmp(const char *_Str1,const char *_Str2,size_t _MaxCount);
               ^~~~~~~
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o biovizBase.dll tmp.def R_init_biovizBase.o bin_offsets.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/biovizBase.buildbin-libdir/biovizBase/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'biovizBase' as biovizBase_1.40.0.zip
* DONE (biovizBase)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'biovizBase' successfully unpacked and MD5 sums checked