Package: Starr

Version: 1.39.0

Command: rm -rf Starr.buildbin-libdir && mkdir Starr.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Starr_1.39.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Starr.buildbin-libdir

StartedAt: 2019-04-09 07:50:34 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 07:51:15 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 41.2 seconds

RetCode: 0

Status:  OK

PackageFile: Starr_1.39.0.tgz

PackageFileSize: 1.689 MiB

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### Running command:
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###   rm -rf Starr.buildbin-libdir && mkdir Starr.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Starr_1.39.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Starr.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Starr.buildbin-libdir Starr_1.39.0.tar.gz'
>>>>>>> 

* installing *source* package ‘Starr’ ...
** using staged installation
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1   -I/usr/local/include  -fPIC  -Wall -g -O2  -c ahocorasick.c -o ahocorasick.o
ahocorasick.c:8:1: warning: unused function 'kseq_rewind' [-Wunused-function]
KSEQ_INIT(gzFile, gzread)
^
./kseq.h:220:2: note: expanded from macro 'KSEQ_INIT'
        __KSEQ_BASIC(type_t)                                            \
        ^
./kseq.h:152:21: note: expanded from macro '__KSEQ_BASIC'
        static inline void kseq_rewind(kseq_t *ks)                                                      \
                           ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1   -I/usr/local/include  -fPIC  -Wall -g -O2  -c collect.c -o collect.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1   -I/usr/local/include  -fPIC  -Wall -g -O2  -c rm_small_peak.c -o rm_small_peak.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1   -I/usr/local/include  -fPIC  -Wall -g -O2  -c sort_by_genomic.c -o sort_by_genomic.o
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 Starr.so ahocorasick.o collect.o rm_small_peak.o sort_by_genomic.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/Starr.buildbin-libdir/00LOCK-Starr/00new/Starr/libs
** R
** 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 (Starr)


>>>>>>> 
>>>>>>> FIXING LINKS FOR Starr.buildbin-libdir/Starr/libs//Starr.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" "Starr.buildbin-libdir/Starr/libs//Starr.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "Starr.buildbin-libdir/Starr/libs//Starr.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" "Starr.buildbin-libdir/Starr/libs//Starr.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "Starr.buildbin-libdir/Starr/libs//Starr.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "Starr.buildbin-libdir/Starr/libs//Starr.so"