Package: HMMcopy

Version: 1.25.0

Command: rm -rf HMMcopy.buildbin-libdir && mkdir HMMcopy.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh HMMcopy_1.25.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R HMMcopy.buildbin-libdir

StartedAt: 2019-04-09 07:11:51 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 07:12:23 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 32.2 seconds

RetCode: 0

Status:  OK

PackageFile: HMMcopy_1.25.0.tgz

PackageFileSize: 1.771 MiB

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### Running command:
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###   rm -rf HMMcopy.buildbin-libdir && mkdir HMMcopy.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh HMMcopy_1.25.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R HMMcopy.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=HMMcopy.buildbin-libdir HMMcopy_1.25.0.tar.gz'
>>>>>>> 

* installing *source* package ‘HMMcopy’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c forward_backward.c -o forward_backward.o
forward_backward.c:28:13: warning: unused variable 'tmp' [-Wunused-variable]
  int K, T, tmp;
            ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c register.c -o register.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -fPIC  -Wall -g -O2  -c viterbi.c -o viterbi.o
viterbi.c:21:13: warning: unused variable 'tmp' [-Wunused-variable]
  int K, T, tmp;
            ^
1 warning generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o HMMcopy.so forward_backward.o register.o viterbi.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/HMMcopy.buildbin-libdir/00LOCK-HMMcopy/00new/HMMcopy/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (HMMcopy)


>>>>>>> 
>>>>>>> FIXING LINKS FOR HMMcopy.buildbin-libdir/HMMcopy/libs//HMMcopy.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgcc_s.1.dylib" "HMMcopy.buildbin-libdir/HMMcopy/libs//HMMcopy.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "HMMcopy.buildbin-libdir/HMMcopy/libs//HMMcopy.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.5.2.dylib" "HMMcopy.buildbin-libdir/HMMcopy/libs//HMMcopy.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "HMMcopy.buildbin-libdir/HMMcopy/libs//HMMcopy.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "HMMcopy.buildbin-libdir/HMMcopy/libs//HMMcopy.so"