Package: deepSNV

Version: 1.26.1

Command: rm -rf deepSNV.buildbin-libdir && mkdir deepSNV.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh deepSNV_1.26.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R deepSNV.buildbin-libdir

StartedAt: 2018-10-17 01:11:58 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 01:13:01 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 63.6 seconds

RetCode: 0

Status:  OK

PackageFile: deepSNV_1.26.1.tgz

PackageFileSize: 2.846 MiB

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### Running command:
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###   rm -rf deepSNV.buildbin-libdir && mkdir deepSNV.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh deepSNV_1.26.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R deepSNV.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=deepSNV.buildbin-libdir deepSNV_1.26.1.tar.gz'
>>>>>>> 

* installing *source* package ‘deepSNV’ ...
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking malloc.h usability... no
checking malloc.h presence... no
checking for malloc.h... no
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for working memcmp... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for off_t... yes
checking for size_t... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c bam2R.cpp -o bam2R.o
bam2R.cpp:79:6: warning: unused variable 'c' [-Wunused-variable]
        int c = 0;
            ^
bam2R.cpp:76:13: warning: unused variable 'iter' [-Wunused-variable]
        hts_itr_t *iter = NULL;
                   ^
2 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c betabinom.c -o betabinom.o
betabinom.c:27:9: warning: unused variable 'log' [-Wunused-variable]
        int i, log=0;
               ^
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 deepSNV.so bam2R.o betabinom.o /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/usrlib/libhts.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.7-bioc/meat/deepSNV.buildbin-libdir/deepSNV/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
* DONE (deepSNV)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgcc_s.1.dylib" "deepSNV.buildbin-libdir/deepSNV/libs//deepSNV.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib" "deepSNV.buildbin-libdir/deepSNV/libs//deepSNV.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.5.2.dylib" "deepSNV.buildbin-libdir/deepSNV/libs//deepSNV.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.dylib" "deepSNV.buildbin-libdir/deepSNV/libs//deepSNV.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib" "deepSNV.buildbin-libdir/deepSNV/libs//deepSNV.so"