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Package 520/609HostnameOS / ArchBUILDCHECKBUILD BIN
rSFFreader 0.6.0
Matt Settles
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/rSFFreader
Last Changed Rev: 70144 / Revision: 74773
Last Changed Date: 2012-10-03 08:43:48 -0700 (Wed, 03 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 N O T   S U P P O R T E D
perceval Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS [ OK ]

Summary

Package: rSFFreader
Version: 0.6.0
Command: rm -rf rSFFreader.buildbin-libdir && mkdir rSFFreader.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh rSFFreader_0.6.0.tar.gz /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R rSFFreader.buildbin-libdir
StartedAt: 2013-03-25 02:05:02 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 02:05:44 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 41.4 seconds
RetCode: 0
Status:  OK 
PackageFile: rSFFreader_0.6.0.tgz
PackageFileSize: 4.465 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=rSFFreader.buildbin-libdir rSFFreader_0.6.0.tar.gz'
>>>>>>> 

* installing *source* package 'rSFFreader' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c R_init_rSFFreader.c -o R_init_rSFFreader.o
R_init_rSFFreader.c:21: warning: ISO C does not allow extra ';' outside of a function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c SFF-io.c -o SFF-io.o
SFF-io.c: In function 'readCommonHeader':
SFF-io.c:280: warning: value computed is not used
SFF-io.c:258: warning: unused variable 'size'
SFF-io.c:250: warning: unused variable 'uint8'
SFF-io.c:249: warning: unused variable 'uint16'
SFF-io.c:247: warning: unused variable 'padding_size'
SFF-io.c: In function 'read_sff':
SFF-io.c:542: warning: 'loader_ext.lkup_length_seq' may be used uninitialized in this function
SFF-io.c:542: note: 'loader_ext.lkup_length_seq' was declared here
SFF-io.c:542: warning: 'loader_ext.lkup_length_qual' may be used uninitialized in this function
SFF-io.c:542: note: 'loader_ext.lkup_length_qual' was declared here
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o rSFFreader.so Biostrings_stubs.o IRanges_stubs.o R_init_rSFFreader.o SFF-io.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/rSFFreader.buildbin-libdir/rSFFreader/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'rSFFreader.Rnw' 
** testing if installed package can be loaded

* DONE (rSFFreader)


>>>>>>> 
>>>>>>> FIXING LINKS FOR rSFFreader.buildbin-libdir/rSFFreader/libs/i386/rSFFreader.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgcc_s.1.dylib" "rSFFreader.buildbin-libdir/rSFFreader/libs/i386/rSFFreader.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "rSFFreader.buildbin-libdir/rSFFreader/libs/i386/rSFFreader.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.5.2.dylib" "rSFFreader.buildbin-libdir/rSFFreader/libs/i386/rSFFreader.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "rSFFreader.buildbin-libdir/rSFFreader/libs/i386/rSFFreader.so"


>>>>>>> 
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --no-multiarch --no-test-load --library=rSFFreader.buildbin-libdir --libs-only rSFFreader_0.6.0.tar.gz'
>>>>>>> 

* installing *source* package 'rSFFreader' ...
** libs
*** arch - x86_64
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c R_init_rSFFreader.c -o R_init_rSFFreader.o
R_init_rSFFreader.c:21: warning: ISO C does not allow extra ';' outside of a function
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c SFF-io.c -o SFF-io.o
SFF-io.c: In function 'readCommonHeader':
SFF-io.c:280: warning: value computed is not used
SFF-io.c:258: warning: unused variable 'size'
SFF-io.c:250: warning: unused variable 'uint8'
SFF-io.c:249: warning: unused variable 'uint16'
SFF-io.c:247: warning: unused variable 'padding_size'
SFF-io.c: In function 'read_sff':
SFF-io.c:542: warning: 'loader_ext.lkup_length_seq' may be used uninitialized in this function
SFF-io.c:542: note: 'loader_ext.lkup_length_seq' was declared here
SFF-io.c:542: warning: 'loader_ext.lkup_length_qual' may be used uninitialized in this function
SFF-io.c:542: note: 'loader_ext.lkup_length_qual' was declared here
gcc -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o rSFFreader.so Biostrings_stubs.o IRanges_stubs.o R_init_rSFFreader.o SFF-io.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/rSFFreader.buildbin-libdir/rSFFreader/libs/x86_64

* DONE (rSFFreader)


>>>>>>> 
>>>>>>> FIXING LINKS FOR rSFFreader.buildbin-libdir/rSFFreader/libs/x86_64/rSFFreader.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgcc_s.1.dylib" "rSFFreader.buildbin-libdir/rSFFreader/libs/x86_64/rSFFreader.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "rSFFreader.buildbin-libdir/rSFFreader/libs/x86_64/rSFFreader.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.5.2.dylib" "rSFFreader.buildbin-libdir/rSFFreader/libs/x86_64/rSFFreader.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "rSFFreader.buildbin-libdir/rSFFreader/libs/x86_64/rSFFreader.so"