ShortRead 1.9.16
Biocore Team c/o BioC user list
| Snapshot Date: 2011-03-17 11:16:30 -0700 (Thu, 17 Mar 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead | | Last Changed Rev: 53541 / Revision: 53825 | | Last Changed Date: 2011-03-09 04:47:01 -0800 (Wed, 09 Mar 2011) |
| lamb1 | Linux (openSUSE 11.3) / x86_64 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
| petty | Mac OS X Snow Leopard (10.6.6) / i386 | OK | WARNINGS | [ OK ] |
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --library=ShortRead.buildbin-libdir ShortRead_1.9.16.tar.gz'
>>>>>>>
* installing *source* package 'ShortRead' ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
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 size of unsigned long... 8
checking for gzeof in -lz... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c alphabet.c -o alphabet.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c io.c -o io.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c io_bowtie.c -o io_bowtie.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c io_soap.c -o io_soap.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c pileup.c -o pileup.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -DHAVE_LIBZ=1 -fPIC -g -O2 -Wall -fasm-blocks -c readBfaToc.cc -o readBfaToc.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -DHAVE_LIBZ=1 -fPIC -g -O2 -Wall -fasm-blocks -c read_maq_map.cc -o read_maq_map.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c sampler.c -o sampler.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c util.c -o util.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c xsnap.c -o xsnap.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o alphabet.o io.o io_bowtie.o io_soap.o pileup.o readBfaToc.o read_maq_map.o sampler.o util.o xsnap.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/ShortRead.buildbin-libdir/ShortRead/libs/i386
** R
** inst
** preparing package for lazy loading
Attaching package: 'IRanges'
The following object(s) are masked from 'package:base':
Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
pmin, pmin.int, rbind, rep.int, setdiff, table, union
Warning: Class "AssayData" is defined (with package slot 'Biobase') but no metadata object found to revise subclass information---not exported? Making a copy in package 'ShortRead'
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (ShortRead)
>>>>>>>
>>>>>>> FIXING LINKS FOR ShortRead.buildbin-libdir/ShortRead/libs/i386/ShortRead.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgcc_s.1.dylib" "ShortRead.buildbin-libdir/ShortRead/libs/i386/ShortRead.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib" "ShortRead.buildbin-libdir/ShortRead/libs/i386/ShortRead.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.5.2.dylib" "ShortRead.buildbin-libdir/ShortRead/libs/i386/ShortRead.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.dylib" "ShortRead.buildbin-libdir/ShortRead/libs/i386/ShortRead.so"
>>>>>>>
>>>>>>> INSTALLATION OF ppc LIBS WITH 'R_ARCH=/ppc R CMD INSTALL --preclean --library=ShortRead.buildbin-libdir --libs-only ShortRead_1.9.16.tar.gz'
>>>>>>>
* installing *source* package 'ShortRead' ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
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 size of unsigned long... 8
checking for gzeof in -lz... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - ppc
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c alphabet.c -o alphabet.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c io.c -o io.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c io_bowtie.c -o io_bowtie.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c io_soap.c -o io_soap.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c pileup.c -o pileup.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -DHAVE_LIBZ=1 -fPIC -g -O2 -Wall -fasm-blocks -c readBfaToc.cc -o readBfaToc.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -DHAVE_LIBZ=1 -fPIC -g -O2 -Wall -fasm-blocks -c read_maq_map.cc -o read_maq_map.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c sampler.c -o sampler.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c util.c -o util.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c xsnap.c -o xsnap.o
g++ -arch ppc -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o alphabet.o io.o io_bowtie.o io_soap.o pileup.o readBfaToc.o read_maq_map.o sampler.o util.o xsnap.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/ShortRead.buildbin-libdir/ShortRead/libs/ppc
* DONE (ShortRead)
>>>>>>>
>>>>>>> FIXING LINKS FOR ShortRead.buildbin-libdir/ShortRead/libs/ppc/ShortRead.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgcc_s.1.dylib" "ShortRead.buildbin-libdir/ShortRead/libs/ppc/ShortRead.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib" "ShortRead.buildbin-libdir/ShortRead/libs/ppc/ShortRead.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.5.2.dylib" "ShortRead.buildbin-libdir/ShortRead/libs/ppc/ShortRead.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.dylib" "ShortRead.buildbin-libdir/ShortRead/libs/ppc/ShortRead.so"
>>>>>>>
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --library=ShortRead.buildbin-libdir --libs-only ShortRead_1.9.16.tar.gz'
>>>>>>>
* installing *source* package 'ShortRead' ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
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 size of unsigned long... 8
checking for gzeof in -lz... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - x86_64
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/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/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c alphabet.c -o alphabet.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c io.c -o io.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c io_bowtie.c -o io_bowtie.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c io_soap.c -o io_soap.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c pileup.c -o pileup.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -DHAVE_LIBZ=1 -fPIC -g -O2 -Wall -fasm-blocks -c readBfaToc.cc -o readBfaToc.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -DHAVE_LIBZ=1 -fPIC -g -O2 -Wall -fasm-blocks -c read_maq_map.cc -o read_maq_map.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c sampler.c -o sampler.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c util.c -o util.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c xsnap.c -o xsnap.o
g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o alphabet.o io.o io_bowtie.o io_soap.o pileup.o readBfaToc.o read_maq_map.o sampler.o util.o xsnap.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/ShortRead.buildbin-libdir/ShortRead/libs/x86_64
* DONE (ShortRead)
>>>>>>>
>>>>>>> FIXING LINKS FOR ShortRead.buildbin-libdir/ShortRead/libs/x86_64/ShortRead.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgcc_s.1.dylib" "ShortRead.buildbin-libdir/ShortRead/libs/x86_64/ShortRead.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib" "ShortRead.buildbin-libdir/ShortRead/libs/x86_64/ShortRead.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.5.2.dylib" "ShortRead.buildbin-libdir/ShortRead/libs/x86_64/ShortRead.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.dylib" "ShortRead.buildbin-libdir/ShortRead/libs/x86_64/ShortRead.so"