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###
### Running command:
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###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/HMMcopy_1.32.0.tar.gz && rm -rf HMMcopy.buildbin-libdir && mkdir HMMcopy.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HMMcopy.buildbin-libdir HMMcopy_1.32.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL HMMcopy_1.32.0.zip && rm HMMcopy_1.32.0.tar.gz HMMcopy_1.32.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  587k  100  587k    0     0  25.0M      0 --:--:-- --:--:-- --:--:-- 26.0M

install for i386

* installing *source* package 'HMMcopy' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c forward_backward.c -o forward_backward.o
forward_backward.c: In function 'forward_backward':
forward_backward.c:28:13: warning: unused variable 'tmp' [-Wunused-variable]
   int K, T, tmp;
             ^~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c register.c -o register.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c viterbi.c -o viterbi.o
viterbi.c: In function 'viterbi':
viterbi.c:21:13: warning: unused variable 'tmp' [-Wunused-variable]
   int K, T, tmp;
             ^~~
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o HMMcopy.dll tmp.def forward_backward.o register.o viterbi.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/HMMcopy.buildbin-libdir/00LOCK-HMMcopy/00new/HMMcopy/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'HMMcopy'
    finding HTML links ... done
    HMMcopy-dataset                         html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpILPuqR/R.INSTALLc3c56f32a73/HMMcopy/man/HMMcopy-dataset.Rd:41: missing file link 'RangedData-class'
    HMMcopy-input                           html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpILPuqR/R.INSTALLc3c56f32a73/HMMcopy/man/HMMcopy-input.Rd:32: missing file link 'RangedData-class'
    HMMcopy-internal                        html  
    HMMcopy-output                          html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpILPuqR/R.INSTALLc3c56f32a73/HMMcopy/man/HMMcopy-output.Rd:18: missing file link 'RangedData-class'
    HMMcopy-package                         html  
    HMMcopy-visualize                       html  
    HMMsegment                              html  
    correctReadcount                        html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpILPuqR/R.INSTALLc3c56f32a73/HMMcopy/man/correctReadcount.Rd:15: missing file link 'RangedData-class'
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpILPuqR/R.INSTALLc3c56f32a73/HMMcopy/man/correctReadcount.Rd:59: missing file link 'RangedData-class'
    wigsToRangedData                        html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpILPuqR/R.INSTALLc3c56f32a73/HMMcopy/man/wigsToRangedData.Rd:41: missing file link 'RangedData-class'
** 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 'HMMcopy' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c forward_backward.c -o forward_backward.o
forward_backward.c: In function 'forward_backward':
forward_backward.c:28:13: warning: unused variable 'tmp' [-Wunused-variable]
   int K, T, tmp;
             ^~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c register.c -o register.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c viterbi.c -o viterbi.o
viterbi.c: In function 'viterbi':
viterbi.c:21:13: warning: unused variable 'tmp' [-Wunused-variable]
   int K, T, tmp;
             ^~~
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o HMMcopy.dll tmp.def forward_backward.o register.o viterbi.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/HMMcopy.buildbin-libdir/HMMcopy/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HMMcopy' as HMMcopy_1.32.0.zip
* DONE (HMMcopy)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'HMMcopy' successfully unpacked and MD5 sums checked