Package: affyio

Version: 1.27.1

Command: rm -rf affyio.buildbin-libdir && mkdir affyio.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh affyio_1.27.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R affyio.buildbin-libdir

StartedAt: 2013-03-25 05:16:19 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 05:16:44 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 24.4 seconds

RetCode: 0

Status:  OK

PackageFile: affyio_1.27.1.tgz

PackageFileSize: 159.6 KiB

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=affyio.buildbin-libdir affyio_1.27.1.tar.gz'
>>>>>>> 

* installing *source* package 'affyio' ...
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 for main in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
checking for pthread_create in -lpthread... yes
checking if we can use pthreads... yes
checking if PTHREAD_STACK_MIN is defined... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -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 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include   -g -O2   -fPIC  -g -O2 -Wall -pedantic  -c fread_functions.c -o fread_functions.o
fread_functions.c:301: warning: 'swap_uint_32' defined but not used
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -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 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include   -g -O2   -fPIC  -g -O2 -Wall -pedantic  -c read_abatch.c -o read_abatch.o
read_abatch.c: In function 'readfile_group':
read_abatch.c:4367: warning: unused variable 'Current_intensity'
read_abatch.c: In function 'checkFileCDF_group':
read_abatch.c:4385: warning: control reaches end of non-void function
read_abatch.c: In function 'readfile_group':
read_abatch.c:4376: warning: control reaches end of non-void function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -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 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include   -g -O2   -fPIC  -g -O2 -Wall -pedantic  -c read_bpmap.c -o read_bpmap.o
read_bpmap.c: In function 'ReadBPMAPHeader':
read_bpmap.c:78: warning: unused variable 'version_number_int'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -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 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include   -g -O2   -fPIC  -g -O2 -Wall -pedantic  -c read_cdf_xda.c -o read_cdf_xda.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -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 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include   -g -O2   -fPIC  -g -O2 -Wall -pedantic  -c read_cdffile2.c -o read_cdffile2.o
read_cdffile2.c:364: warning: 'token_ends_with' defined but not used
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -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 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include   -g -O2   -fPIC  -g -O2 -Wall -pedantic  -c read_celfile_generic.c -o read_celfile_generic.o
read_celfile_generic.c: In function 'read_genericcel_file_intensities':
read_celfile_generic.c:710: warning: unused variable 'fread_err'
read_celfile_generic.c:708: warning: unused variable 'cur_index'
read_celfile_generic.c:707: warning: unused variable 'j'
read_celfile_generic.c: In function 'read_genericcel_file_stddev':
read_celfile_generic.c:760: warning: unused variable 'fread_err'
read_celfile_generic.c:758: warning: unused variable 'cur_index'
read_celfile_generic.c:757: warning: unused variable 'j'
read_celfile_generic.c: In function 'read_genericcel_file_npixels':
read_celfile_generic.c:814: warning: unused variable 'fread_err'
read_celfile_generic.c:812: warning: unused variable 'cur_index'
read_celfile_generic.c:811: warning: unused variable 'j'
read_celfile_generic.c: In function 'generic_get_masks_outliers':
read_celfile_generic.c:876: warning: unused variable 'fread_err'
read_celfile_generic.c:874: warning: unused variable 'cur_index'
read_celfile_generic.c:873: warning: unused variable 'j'
read_celfile_generic.c: In function 'generic_apply_masks':
read_celfile_generic.c:968: warning: unused variable 'fread_err'
read_celfile_generic.c:962: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzread_genericcel_file_intensities':
read_celfile_generic.c:1714: warning: unused variable 'fread_err'
read_celfile_generic.c:1712: warning: unused variable 'cur_index'
read_celfile_generic.c:1711: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzread_genericcel_file_stddev':
read_celfile_generic.c:1765: warning: unused variable 'fread_err'
read_celfile_generic.c:1763: warning: unused variable 'cur_index'
read_celfile_generic.c:1762: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzread_genericcel_file_npixels':
read_celfile_generic.c:1819: warning: unused variable 'fread_err'
read_celfile_generic.c:1817: warning: unused variable 'cur_index'
read_celfile_generic.c:1816: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzgeneric_get_masks_outliers':
read_celfile_generic.c:1884: warning: unused variable 'fread_err'
read_celfile_generic.c:1882: warning: unused variable 'cur_index'
read_celfile_generic.c:1881: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzgeneric_apply_masks':
read_celfile_generic.c:1976: warning: unused variable 'fread_err'
read_celfile_generic.c:1970: warning: unused variable 'j'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -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 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include   -g -O2   -fPIC  -g -O2 -Wall -pedantic  -c read_clf.c -o read_clf.o
read_clf.c: In function 'read_clf_header':
read_clf.c:557: warning: unused variable 'i'
read_clf.c: At top level:
read_clf.c:292: warning: 'token_ends_with' defined but not used
read_clf.c:389: warning: 'IsCommentLine' defined but not used
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -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 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include   -g -O2   -fPIC  -g -O2 -Wall -pedantic  -c read_generic.c -o read_generic.o
read_generic.c: In function 'decode_nvt_triplet':
read_generic.c:1683: warning: control reaches end of non-void function
read_generic.c: In function 'determine_MIMETYPE':
read_generic.c:458: warning: control reaches end of non-void function
read_generic.c: In function 'Read_Generic_R_List':
read_generic.c:1877: warning: 'return_value' may be used uninitialized in this function
read_generic.c:1877: note: 'return_value' was declared here
read_generic.c:1782: warning: 'tmp_sexp' may be used uninitialized in this function
read_generic.c:1782: note: 'tmp_sexp' was declared here
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -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 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include   -g -O2   -fPIC  -g -O2 -Wall -pedantic  -c read_multichannel_celfile_generic.c -o read_multichannel_celfile_generic.o
read_multichannel_celfile_generic.c: In function 'multichannel_determine_number_channels':
read_multichannel_celfile_generic.c:109: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:106: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:105: warning: unused variable 'k'
read_multichannel_celfile_generic.c:105: warning: unused variable 'i'
read_multichannel_celfile_generic.c: In function 'multichannel_determine_channel_name':
read_multichannel_celfile_generic.c:173: warning: unused variable 'my_data_set'
read_multichannel_celfile_generic.c:165: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:162: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:161: warning: unused variable 'j'
read_multichannel_celfile_generic.c:161: warning: unused variable 'i'
read_multichannel_celfile_generic.c: In function 'read_genericcel_file_intensities_multichannel':
read_multichannel_celfile_generic.c:223: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:221: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:220: warning: unused variable 'j'
read_multichannel_celfile_generic.c: In function 'read_genericcel_file_stddev_multichannel':
read_multichannel_celfile_generic.c:280: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:278: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:277: warning: unused variable 'j'
read_multichannel_celfile_generic.c: In function 'read_genericcel_file_npixels_multichannel':
read_multichannel_celfile_generic.c:344: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:342: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:341: warning: unused variable 'j'
read_multichannel_celfile_generic.c: In function 'generic_get_masks_outliers_multichannel':
read_multichannel_celfile_generic.c:418: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:416: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:415: warning: unused variable 'j'
read_multichannel_celfile_generic.c: In function 'generic_apply_masks_multichannel':
read_multichannel_celfile_generic.c:522: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:516: warning: unused variable 'j'
read_multichannel_celfile_generic.c: In function 'gzmultichannel_determine_number_channels':
read_multichannel_celfile_generic.c:664: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:661: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:660: warning: unused variable 'k'
read_multichannel_celfile_generic.c:660: warning: unused variable 'i'
read_multichannel_celfile_generic.c: In function 'gzmultichannel_determine_channel_name':
read_multichannel_celfile_generic.c:725: warning: unused variable 'my_data_set'
read_multichannel_celfile_generic.c:717: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:714: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:713: warning: unused variable 'j'
read_multichannel_celfile_generic.c:713: warning: unused variable 'i'
read_multichannel_celfile_generic.c: In function 'gzread_genericcel_file_intensities_multichannel':
read_multichannel_celfile_generic.c:766: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:764: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:763: warning: unused variable 'j'
read_multichannel_celfile_generic.c: In function 'gzread_genericcel_file_stddev_multichannel':
read_multichannel_celfile_generic.c:822: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:820: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:819: warning: unused variable 'j'
read_multichannel_celfile_generic.c: In function 'gzread_genericcel_file_npixels_multichannel':
read_multichannel_celfile_generic.c:884: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:882: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:881: warning: unused variable 'j'
read_multichannel_celfile_generic.c: In function 'gzgeneric_get_masks_outliers_multichannel':
read_multichannel_celfile_generic.c:953: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:951: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:950: warning: unused variable 'j'
read_multichannel_celfile_generic.c: In function 'gzgeneric_apply_masks_multichannel':
read_multichannel_celfile_generic.c:1055: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:1049: warning: unused variable 'j'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -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 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include   -g -O2   -fPIC  -g -O2 -Wall -pedantic  -c read_pgf.c -o read_pgf.o
read_pgf.c: In function 'read_pgf_header':
read_pgf.c:901: warning: unused variable 'i'
read_pgf.c: In function 'insert_level0':
read_pgf.c:1167: warning: unused variable 'temp_ptr'
read_pgf.c: In function 'pgf_count_probeset_types':
read_pgf.c:1265: warning: assignment from incompatible pointer type
read_pgf.c: At top level:
read_pgf.c:363: warning: 'token_ends_with' defined but not used
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o affyio.so fread_functions.o read_abatch.o read_bpmap.o read_cdf_xda.o read_cdffile2.o read_celfile_generic.o read_clf.o read_generic.o read_multichannel_celfile_generic.o read_pgf.o -lpthread -lz -lpthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/affyio.buildbin-libdir/affyio/libs/i386
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (affyio)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgcc_s.1.dylib" "affyio.buildbin-libdir/affyio/libs/i386/affyio.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "affyio.buildbin-libdir/affyio/libs/i386/affyio.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.5.2.dylib" "affyio.buildbin-libdir/affyio/libs/i386/affyio.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "affyio.buildbin-libdir/affyio/libs/i386/affyio.so"


>>>>>>> 
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --no-multiarch --no-test-load --library=affyio.buildbin-libdir --libs-only affyio_1.27.1.tar.gz'
>>>>>>> 

* installing *source* package 'affyio' ...
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 for main in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
checking for pthread_create in -lpthread... yes
checking if we can use pthreads... yes
checking if PTHREAD_STACK_MIN is defined... 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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -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 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include   -g -O2   -fPIC  -g -O2 -Wall -pedantic  -c fread_functions.c -o fread_functions.o
fread_functions.c:301: warning: 'swap_uint_32' defined but not used
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -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 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include   -g -O2   -fPIC  -g -O2 -Wall -pedantic  -c read_abatch.c -o read_abatch.o
read_abatch.c: In function 'readfile_group':
read_abatch.c:4367: warning: unused variable 'Current_intensity'
read_abatch.c: In function 'checkFileCDF_group':
read_abatch.c:4385: warning: control reaches end of non-void function
read_abatch.c: In function 'readfile_group':
read_abatch.c:4376: warning: control reaches end of non-void function
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -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 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include   -g -O2   -fPIC  -g -O2 -Wall -pedantic  -c read_bpmap.c -o read_bpmap.o
read_bpmap.c: In function 'ReadBPMAPHeader':
read_bpmap.c:78: warning: unused variable 'version_number_int'
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -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 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include   -g -O2   -fPIC  -g -O2 -Wall -pedantic  -c read_cdf_xda.c -o read_cdf_xda.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -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 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include   -g -O2   -fPIC  -g -O2 -Wall -pedantic  -c read_cdffile2.c -o read_cdffile2.o
read_cdffile2.c:364: warning: 'token_ends_with' defined but not used
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -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 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include   -g -O2   -fPIC  -g -O2 -Wall -pedantic  -c read_celfile_generic.c -o read_celfile_generic.o
read_celfile_generic.c: In function 'read_genericcel_file_intensities':
read_celfile_generic.c:710: warning: unused variable 'fread_err'
read_celfile_generic.c:708: warning: unused variable 'cur_index'
read_celfile_generic.c:707: warning: unused variable 'j'
read_celfile_generic.c: In function 'read_genericcel_file_stddev':
read_celfile_generic.c:760: warning: unused variable 'fread_err'
read_celfile_generic.c:758: warning: unused variable 'cur_index'
read_celfile_generic.c:757: warning: unused variable 'j'
read_celfile_generic.c: In function 'read_genericcel_file_npixels':
read_celfile_generic.c:814: warning: unused variable 'fread_err'
read_celfile_generic.c:812: warning: unused variable 'cur_index'
read_celfile_generic.c:811: warning: unused variable 'j'
read_celfile_generic.c: In function 'generic_get_masks_outliers':
read_celfile_generic.c:876: warning: unused variable 'fread_err'
read_celfile_generic.c:874: warning: unused variable 'cur_index'
read_celfile_generic.c:873: warning: unused variable 'j'
read_celfile_generic.c: In function 'generic_apply_masks':
read_celfile_generic.c:968: warning: unused variable 'fread_err'
read_celfile_generic.c:962: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzread_genericcel_file_intensities':
read_celfile_generic.c:1714: warning: unused variable 'fread_err'
read_celfile_generic.c:1712: warning: unused variable 'cur_index'
read_celfile_generic.c:1711: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzread_genericcel_file_stddev':
read_celfile_generic.c:1765: warning: unused variable 'fread_err'
read_celfile_generic.c:1763: warning: unused variable 'cur_index'
read_celfile_generic.c:1762: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzread_genericcel_file_npixels':
read_celfile_generic.c:1819: warning: unused variable 'fread_err'
read_celfile_generic.c:1817: warning: unused variable 'cur_index'
read_celfile_generic.c:1816: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzgeneric_get_masks_outliers':
read_celfile_generic.c:1884: warning: unused variable 'fread_err'
read_celfile_generic.c:1882: warning: unused variable 'cur_index'
read_celfile_generic.c:1881: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzgeneric_apply_masks':
read_celfile_generic.c:1976: warning: unused variable 'fread_err'
read_celfile_generic.c:1970: warning: unused variable 'j'
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -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 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include   -g -O2   -fPIC  -g -O2 -Wall -pedantic  -c read_clf.c -o read_clf.o
read_clf.c: In function 'read_clf_header':
read_clf.c:557: warning: unused variable 'i'
read_clf.c: At top level:
read_clf.c:292: warning: 'token_ends_with' defined but not used
read_clf.c:389: warning: 'IsCommentLine' defined but not used
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -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 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include   -g -O2   -fPIC  -g -O2 -Wall -pedantic  -c read_generic.c -o read_generic.o
read_generic.c: In function 'decode_nvt_triplet':
read_generic.c:1683: warning: control reaches end of non-void function
read_generic.c: In function 'determine_MIMETYPE':
read_generic.c:458: warning: control reaches end of non-void function
read_generic.c: In function 'Read_Generic_R_List':
read_generic.c:1782: warning: 'tmp_sexp' may be used uninitialized in this function
read_generic.c:1782: note: 'tmp_sexp' was declared here
read_generic.c:1877: warning: 'return_value' may be used uninitialized in this function
read_generic.c:1877: note: 'return_value' was declared here
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -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 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include   -g -O2   -fPIC  -g -O2 -Wall -pedantic  -c read_multichannel_celfile_generic.c -o read_multichannel_celfile_generic.o
read_multichannel_celfile_generic.c: In function 'multichannel_determine_number_channels':
read_multichannel_celfile_generic.c:109: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:106: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:105: warning: unused variable 'k'
read_multichannel_celfile_generic.c:105: warning: unused variable 'i'
read_multichannel_celfile_generic.c: In function 'multichannel_determine_channel_name':
read_multichannel_celfile_generic.c:173: warning: unused variable 'my_data_set'
read_multichannel_celfile_generic.c:165: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:162: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:161: warning: unused variable 'j'
read_multichannel_celfile_generic.c:161: warning: unused variable 'i'
read_multichannel_celfile_generic.c: In function 'read_genericcel_file_intensities_multichannel':
read_multichannel_celfile_generic.c:223: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:221: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:220: warning: unused variable 'j'
read_multichannel_celfile_generic.c: In function 'read_genericcel_file_stddev_multichannel':
read_multichannel_celfile_generic.c:280: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:278: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:277: warning: unused variable 'j'
read_multichannel_celfile_generic.c: In function 'read_genericcel_file_npixels_multichannel':
read_multichannel_celfile_generic.c:344: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:342: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:341: warning: unused variable 'j'
read_multichannel_celfile_generic.c: In function 'generic_get_masks_outliers_multichannel':
read_multichannel_celfile_generic.c:418: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:416: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:415: warning: unused variable 'j'
read_multichannel_celfile_generic.c: In function 'generic_apply_masks_multichannel':
read_multichannel_celfile_generic.c:522: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:516: warning: unused variable 'j'
read_multichannel_celfile_generic.c: In function 'gzmultichannel_determine_number_channels':
read_multichannel_celfile_generic.c:664: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:661: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:660: warning: unused variable 'k'
read_multichannel_celfile_generic.c:660: warning: unused variable 'i'
read_multichannel_celfile_generic.c: In function 'gzmultichannel_determine_channel_name':
read_multichannel_celfile_generic.c:725: warning: unused variable 'my_data_set'
read_multichannel_celfile_generic.c:717: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:714: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:713: warning: unused variable 'j'
read_multichannel_celfile_generic.c:713: warning: unused variable 'i'
read_multichannel_celfile_generic.c: In function 'gzread_genericcel_file_intensities_multichannel':
read_multichannel_celfile_generic.c:766: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:764: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:763: warning: unused variable 'j'
read_multichannel_celfile_generic.c: In function 'gzread_genericcel_file_stddev_multichannel':
read_multichannel_celfile_generic.c:822: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:820: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:819: warning: unused variable 'j'
read_multichannel_celfile_generic.c: In function 'gzread_genericcel_file_npixels_multichannel':
read_multichannel_celfile_generic.c:884: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:882: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:881: warning: unused variable 'j'
read_multichannel_celfile_generic.c: In function 'gzgeneric_get_masks_outliers_multichannel':
read_multichannel_celfile_generic.c:953: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:951: warning: unused variable 'cur_index'
read_multichannel_celfile_generic.c:950: warning: unused variable 'j'
read_multichannel_celfile_generic.c: In function 'gzgeneric_apply_masks_multichannel':
read_multichannel_celfile_generic.c:1055: warning: unused variable 'fread_err'
read_multichannel_celfile_generic.c:1049: warning: unused variable 'j'
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -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 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include   -g -O2   -fPIC  -g -O2 -Wall -pedantic  -c read_pgf.c -o read_pgf.o
read_pgf.c: In function 'read_pgf_header':
read_pgf.c:901: warning: unused variable 'i'
read_pgf.c: In function 'insert_level0':
read_pgf.c:1167: warning: unused variable 'temp_ptr'
read_pgf.c: In function 'pgf_count_probeset_types':
read_pgf.c:1265: warning: assignment from incompatible pointer type
read_pgf.c: At top level:
read_pgf.c:363: warning: 'token_ends_with' defined but not used
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 affyio.so fread_functions.o read_abatch.o read_bpmap.o read_cdf_xda.o read_cdffile2.o read_celfile_generic.o read_clf.o read_generic.o read_multichannel_celfile_generic.o read_pgf.o -lpthread -lz -lpthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/affyio.buildbin-libdir/affyio/libs/x86_64
* DONE (affyio)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgcc_s.1.dylib" "affyio.buildbin-libdir/affyio/libs/x86_64/affyio.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "affyio.buildbin-libdir/affyio/libs/x86_64/affyio.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.5.2.dylib" "affyio.buildbin-libdir/affyio/libs/x86_64/affyio.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "affyio.buildbin-libdir/affyio/libs/x86_64/affyio.so"