Rsamtools 1.4.3
Biocore Team c/o BioC user list
| Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/Rsamtools | | Last Changed Rev: 57073 / Revision: 59457 | | Last Changed Date: 2011-07-28 06:22:35 -0700 (Thu, 28 Jul 2011) |
| lamb1 | Linux (openSUSE 11.3) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | [ OK ] |
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --library=Rsamtools.buildbin-libdir Rsamtools_1.4.3.tar.gz'
>>>>>>>
* installing *source* package 'Rsamtools' ...
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 for gzeof in -lz... yes
checking for bzero... yes
checking for memset... yes
checking for pow... yes
checking for sqrt... yes
checking for strcasecmp... yes
checking for strdup... yes
checking for strstr... yes
checking for strtol... yes
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 zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.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 ptrdiff_t... 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
config.status: creating src/Rsamtools.mk
** libs
*** arch - i386
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c R_init_Rsamtools.c -o R_init_Rsamtools.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c as_bam.c -o as_bam.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c bamfile.c -o bamfile.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c bcffile.c -o bcffile.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c encode.c -o encode.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c fafile.c -o fafile.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c io_sam.c -o io_sam.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools_patch.c -o samtools_patch.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c utilities.c -o utilities.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bgzf.c -o samtools/bgzf.o
samtools/bgzf.c: In function 'deflate_block':
samtools/bgzf.c:332: warning: pointer of type 'void *' used in arithmetic
samtools/bgzf.c: In function 'inflate_block':
samtools/bgzf.c:349: warning: pointer of type 'void *' used in arithmetic
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/kstring.c -o samtools/kstring.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bam_aux.c -o samtools/bam_aux.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bam.c -o samtools/bam.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bam_import.c -o samtools/bam_import.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/sam.c -o samtools/sam.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bam_index.c -o samtools/bam_index.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bam_pileup.c -o samtools/bam_pileup.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bam_md.c -o samtools/bam_md.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/glf.c -o samtools/glf.o
In file included from samtools/glf.c:3:
samtools/glf.h:5: warning: type of bit-field 'ref_base' is a GCC extension
samtools/glf.h:5: warning: type of bit-field 'dummy' is a GCC extension
In file included from samtools/glf.c:3:
samtools/glf.h:20: warning: type of bit-field 'ref_base' is a GCC extension
samtools/glf.h:20: warning: type of bit-field 'rtype' is a GCC extension
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/razf.c -o samtools/razf.o
samtools/razf.c: In function '_razf_buffered_write':
samtools/razf.c:283: warning: pointer of type 'void *' used in arithmetic
samtools/razf.c: In function 'razf_write':
samtools/razf.c:297: warning: pointer of type 'void *' used in arithmetic
samtools/razf.c: In function 'razf_open_r':
samtools/razf.c:392: warning: pointer of type 'void *' used in arithmetic
samtools/razf.c:400: warning: pointer of type 'void *' used in arithmetic
samtools/razf.c: In function '_razf_open':
samtools/razf.c:511: warning: ordered comparison of pointer with integer zero
samtools/razf.c: In function 'razf_read':
samtools/razf.c:631: warning: pointer of type 'void *' used in arithmetic
samtools/razf.c:637: warning: pointer of type 'void *' used in arithmetic
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/faidx.c -o samtools/faidx.o
samtools/faidx.c:10: warning: type of bit-field 'len' is a GCC extension
samtools/faidx.c:10: warning: type of bit-field 'line_len' is a GCC extension
samtools/faidx.c:10: warning: type of bit-field 'line_blen' is a GCC extension
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/knetfile.c -o samtools/knetfile.o
samtools/knetfile.c: In function 'my_netread':
samtools/knetfile.c:189: warning: pointer of type 'void *' used in arithmetic
samtools/knetfile.c: In function 'knet_read':
samtools/knetfile.c:520: warning: pointer of type 'void *' used in arithmetic
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bam_sort.c -o samtools/bam_sort.o
samtools/bam_sort.c: In function '__ks_insertsort_heap':
samtools/bam_sort.c:53: warning: 'heap_lt' is static but used in inline function '__ks_insertsort_heap' which is not static
samtools/bam_sort.c: In function '__ks_insertsort_sort':
samtools/bam_sort.c:297: warning: 'bam1_lt' is static but used in inline function '__ks_insertsort_sort' which is not static
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/sam_header.c -o samtools/sam_header.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bam_reheader.c -o samtools/bam_reheader.o
samtools/bam_reheader.c: In function 'bam_reheader':
samtools/bam_reheader.c:20: warning: pointer of type 'void *' used in arithmetic
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/kprobaln.c -o samtools/kprobaln.o
ar -crus libbam.a samtools/bgzf.o samtools/kstring.o samtools/bam_aux.o samtools/bam.o samtools/bam_import.o samtools/sam.o samtools/bam_index.o samtools/bam_pileup.o samtools/bam_lpileup.o samtools/bam_md.o samtools/glf.o samtools/razf.o samtools/faidx.o samtools/knetfile.o samtools/bam_sort.o samtools/sam_header.o samtools/bam_reheader.o samtools/kprobaln.o samtools_patch.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/ld.c -o samtools/bcftools/ld.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/kfunc.c -o samtools/bcftools/kfunc.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/index.c -o samtools/bcftools/index.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/fet.c -o samtools/bcftools/fet.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/bcf2qcall.c -o samtools/bcftools/bcf2qcall.o
samtools/bcftools/bcf2qcall.c: In function 'bcf_2qcall':
samtools/bcftools/bcf2qcall.c:70: warning: pointer of type 'void *' used in arithmetic
ar -crus libbcf.a samtools/bcftools/bcf.o samtools/bcftools/vcf.o samtools/bcftools/bcfutils.o samtools/bcftools/prob1.o samtools/bcftools/ld.o samtools/bcftools/kfunc.o samtools/bcftools/index.o samtools/bcftools/fet.o samtools/bcftools/bcf2qcall.o samtools_patch.o
mkdir -p /Users/biocbuild/bbs-2.8-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/i386
cp Rsamtools.mk /Users/biocbuild/bbs-2.8-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/i386
mkdir -p /Users/biocbuild/bbs-2.8-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools
cp samtools/*.h /Users/biocbuild/bbs-2.8-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/
cp samtools/bcftools/*h /Users/biocbuild/bbs-2.8-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools/
mkdir -p /Users/biocbuild/bbs-2.8-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386
cp libbam.a libbcf.a /Users/biocbuild/bbs-2.8-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o Rsamtools.so Biostrings_stubs.o IRanges_stubs.o R_init_Rsamtools.o as_bam.o bamfile.o bcffile.o encode.o fafile.o io_sam.o samtools_patch.o utilities.o -L. -lbam -lbcf -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (Rsamtools)
>>>>>>>
>>>>>>> FIXING LINKS FOR Rsamtools.buildbin-libdir/Rsamtools/libs/i386/Rsamtools.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" "Rsamtools.buildbin-libdir/Rsamtools/libs/i386/Rsamtools.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib" "Rsamtools.buildbin-libdir/Rsamtools/libs/i386/Rsamtools.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" "Rsamtools.buildbin-libdir/Rsamtools/libs/i386/Rsamtools.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.dylib" "Rsamtools.buildbin-libdir/Rsamtools/libs/i386/Rsamtools.so"
>>>>>>>
>>>>>>> INSTALLATION OF ppc LIBS WITH 'R_ARCH=/ppc R CMD INSTALL --preclean --library=Rsamtools.buildbin-libdir --libs-only Rsamtools_1.4.3.tar.gz'
>>>>>>>
* installing *source* package 'Rsamtools' ...
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 for gzeof in -lz... yes
checking for bzero... yes
checking for memset... yes
checking for pow... yes
checking for sqrt... yes
checking for strcasecmp... yes
checking for strdup... yes
checking for strstr... yes
checking for strtol... yes
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 zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.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 ptrdiff_t... 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
config.status: creating src/Rsamtools.mk
** libs
*** arch - ppc
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c R_init_Rsamtools.c -o R_init_Rsamtools.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c as_bam.c -o as_bam.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c bamfile.c -o bamfile.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c bcffile.c -o bcffile.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c encode.c -o encode.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c fafile.c -o fafile.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c io_sam.c -o io_sam.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools_patch.c -o samtools_patch.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c utilities.c -o utilities.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bgzf.c -o samtools/bgzf.o
samtools/bgzf.c: In function 'deflate_block':
samtools/bgzf.c:332: warning: pointer of type 'void *' used in arithmetic
samtools/bgzf.c: In function 'inflate_block':
samtools/bgzf.c:349: warning: pointer of type 'void *' used in arithmetic
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/kstring.c -o samtools/kstring.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bam_aux.c -o samtools/bam_aux.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bam.c -o samtools/bam.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bam_import.c -o samtools/bam_import.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/sam.c -o samtools/sam.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bam_index.c -o samtools/bam_index.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bam_pileup.c -o samtools/bam_pileup.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bam_md.c -o samtools/bam_md.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/glf.c -o samtools/glf.o
In file included from samtools/glf.c:3:
samtools/glf.h:5: warning: type of bit-field 'ref_base' is a GCC extension
samtools/glf.h:5: warning: type of bit-field 'dummy' is a GCC extension
In file included from samtools/glf.c:3:
samtools/glf.h:20: warning: type of bit-field 'ref_base' is a GCC extension
samtools/glf.h:20: warning: type of bit-field 'rtype' is a GCC extension
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/razf.c -o samtools/razf.o
samtools/razf.c: In function '_razf_buffered_write':
samtools/razf.c:283: warning: pointer of type 'void *' used in arithmetic
samtools/razf.c: In function 'razf_write':
samtools/razf.c:297: warning: pointer of type 'void *' used in arithmetic
samtools/razf.c: In function 'razf_open_r':
samtools/razf.c:392: warning: pointer of type 'void *' used in arithmetic
samtools/razf.c:400: warning: pointer of type 'void *' used in arithmetic
samtools/razf.c: In function '_razf_open':
samtools/razf.c:511: warning: ordered comparison of pointer with integer zero
samtools/razf.c: In function 'razf_read':
samtools/razf.c:631: warning: pointer of type 'void *' used in arithmetic
samtools/razf.c:637: warning: pointer of type 'void *' used in arithmetic
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/faidx.c -o samtools/faidx.o
samtools/faidx.c:10: warning: type of bit-field 'len' is a GCC extension
samtools/faidx.c:10: warning: type of bit-field 'line_len' is a GCC extension
samtools/faidx.c:10: warning: type of bit-field 'line_blen' is a GCC extension
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/knetfile.c -o samtools/knetfile.o
samtools/knetfile.c: In function 'my_netread':
samtools/knetfile.c:189: warning: pointer of type 'void *' used in arithmetic
samtools/knetfile.c: In function 'knet_read':
samtools/knetfile.c:520: warning: pointer of type 'void *' used in arithmetic
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bam_sort.c -o samtools/bam_sort.o
samtools/bam_sort.c: In function '__ks_insertsort_heap':
samtools/bam_sort.c:53: warning: 'heap_lt' is static but used in inline function '__ks_insertsort_heap' which is not static
samtools/bam_sort.c: In function '__ks_insertsort_sort':
samtools/bam_sort.c:297: warning: 'bam1_lt' is static but used in inline function '__ks_insertsort_sort' which is not static
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/sam_header.c -o samtools/sam_header.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bam_reheader.c -o samtools/bam_reheader.o
samtools/bam_reheader.c: In function 'bam_reheader':
samtools/bam_reheader.c:20: warning: pointer of type 'void *' used in arithmetic
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/kprobaln.c -o samtools/kprobaln.o
ar -crus libbam.a samtools/bgzf.o samtools/kstring.o samtools/bam_aux.o samtools/bam.o samtools/bam_import.o samtools/sam.o samtools/bam_index.o samtools/bam_pileup.o samtools/bam_lpileup.o samtools/bam_md.o samtools/glf.o samtools/razf.o samtools/faidx.o samtools/knetfile.o samtools/bam_sort.o samtools/sam_header.o samtools/bam_reheader.o samtools/kprobaln.o samtools_patch.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/ld.c -o samtools/bcftools/ld.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/kfunc.c -o samtools/bcftools/kfunc.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/index.c -o samtools/bcftools/index.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/fet.c -o samtools/bcftools/fet.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/bcf2qcall.c -o samtools/bcftools/bcf2qcall.o
samtools/bcftools/bcf2qcall.c: In function 'bcf_2qcall':
samtools/bcftools/bcf2qcall.c:70: warning: pointer of type 'void *' used in arithmetic
ar -crus libbcf.a samtools/bcftools/bcf.o samtools/bcftools/vcf.o samtools/bcftools/bcfutils.o samtools/bcftools/prob1.o samtools/bcftools/ld.o samtools/bcftools/kfunc.o samtools/bcftools/index.o samtools/bcftools/fet.o samtools/bcftools/bcf2qcall.o samtools_patch.o
mkdir -p /Users/biocbuild/bbs-2.8-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/ppc
cp Rsamtools.mk /Users/biocbuild/bbs-2.8-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/ppc
mkdir -p /Users/biocbuild/bbs-2.8-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools
cp samtools/*.h /Users/biocbuild/bbs-2.8-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/
cp samtools/bcftools/*h /Users/biocbuild/bbs-2.8-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools/
mkdir -p /Users/biocbuild/bbs-2.8-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/ppc
cp libbam.a libbcf.a /Users/biocbuild/bbs-2.8-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/ppc
gcc-4.2 -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o Rsamtools.so Biostrings_stubs.o IRanges_stubs.o R_init_Rsamtools.o as_bam.o bamfile.o bcffile.o encode.o fafile.o io_sam.o samtools_patch.o utilities.o -L. -lbam -lbcf -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/libs/ppc
* DONE (Rsamtools)
>>>>>>>
>>>>>>> FIXING LINKS FOR Rsamtools.buildbin-libdir/Rsamtools/libs/ppc/Rsamtools.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" "Rsamtools.buildbin-libdir/Rsamtools/libs/ppc/Rsamtools.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib" "Rsamtools.buildbin-libdir/Rsamtools/libs/ppc/Rsamtools.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" "Rsamtools.buildbin-libdir/Rsamtools/libs/ppc/Rsamtools.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.dylib" "Rsamtools.buildbin-libdir/Rsamtools/libs/ppc/Rsamtools.so"
>>>>>>>
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --library=Rsamtools.buildbin-libdir --libs-only Rsamtools_1.4.3.tar.gz'
>>>>>>>
* installing *source* package 'Rsamtools' ...
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 for gzeof in -lz... yes
checking for bzero... yes
checking for memset... yes
checking for pow... yes
checking for sqrt... yes
checking for strcasecmp... yes
checking for strdup... yes
checking for strstr... yes
checking for strtol... yes
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 zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.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 ptrdiff_t... 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
config.status: creating src/Rsamtools.mk
** libs
*** arch - x86_64
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c R_init_Rsamtools.c -o R_init_Rsamtools.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c as_bam.c -o as_bam.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c bamfile.c -o bamfile.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c bcffile.c -o bcffile.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c encode.c -o encode.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c fafile.c -o fafile.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c io_sam.c -o io_sam.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools_patch.c -o samtools_patch.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c utilities.c -o utilities.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bgzf.c -o samtools/bgzf.o
samtools/bgzf.c: In function 'deflate_block':
samtools/bgzf.c:332: warning: pointer of type 'void *' used in arithmetic
samtools/bgzf.c: In function 'inflate_block':
samtools/bgzf.c:349: warning: pointer of type 'void *' used in arithmetic
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/kstring.c -o samtools/kstring.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bam_aux.c -o samtools/bam_aux.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bam.c -o samtools/bam.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bam_import.c -o samtools/bam_import.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/sam.c -o samtools/sam.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bam_index.c -o samtools/bam_index.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bam_pileup.c -o samtools/bam_pileup.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bam_md.c -o samtools/bam_md.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/glf.c -o samtools/glf.o
In file included from samtools/glf.c:3:
samtools/glf.h:5: warning: type of bit-field 'ref_base' is a GCC extension
samtools/glf.h:5: warning: type of bit-field 'dummy' is a GCC extension
In file included from samtools/glf.c:3:
samtools/glf.h:20: warning: type of bit-field 'ref_base' is a GCC extension
samtools/glf.h:20: warning: type of bit-field 'rtype' is a GCC extension
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/razf.c -o samtools/razf.o
samtools/razf.c: In function '_razf_buffered_write':
samtools/razf.c:283: warning: pointer of type 'void *' used in arithmetic
samtools/razf.c: In function 'razf_write':
samtools/razf.c:297: warning: pointer of type 'void *' used in arithmetic
samtools/razf.c: In function 'razf_open_r':
samtools/razf.c:392: warning: pointer of type 'void *' used in arithmetic
samtools/razf.c:400: warning: pointer of type 'void *' used in arithmetic
samtools/razf.c: In function '_razf_open':
samtools/razf.c:511: warning: ordered comparison of pointer with integer zero
samtools/razf.c: In function 'razf_read':
samtools/razf.c:631: warning: pointer of type 'void *' used in arithmetic
samtools/razf.c:637: warning: pointer of type 'void *' used in arithmetic
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/faidx.c -o samtools/faidx.o
samtools/faidx.c:10: warning: type of bit-field 'len' is a GCC extension
samtools/faidx.c:10: warning: type of bit-field 'line_len' is a GCC extension
samtools/faidx.c:10: warning: type of bit-field 'line_blen' is a GCC extension
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/knetfile.c -o samtools/knetfile.o
samtools/knetfile.c: In function 'my_netread':
samtools/knetfile.c:189: warning: pointer of type 'void *' used in arithmetic
samtools/knetfile.c: In function 'knet_read':
samtools/knetfile.c:520: warning: pointer of type 'void *' used in arithmetic
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bam_sort.c -o samtools/bam_sort.o
samtools/bam_sort.c: In function '__ks_insertsort_heap':
samtools/bam_sort.c:53: warning: 'heap_lt' is static but used in inline function '__ks_insertsort_heap' which is not static
samtools/bam_sort.c: In function '__ks_insertsort_sort':
samtools/bam_sort.c:297: warning: 'bam1_lt' is static but used in inline function '__ks_insertsort_sort' which is not static
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/sam_header.c -o samtools/sam_header.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bam_reheader.c -o samtools/bam_reheader.o
samtools/bam_reheader.c: In function 'bam_reheader':
samtools/bam_reheader.c:20: warning: pointer of type 'void *' used in arithmetic
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/kprobaln.c -o samtools/kprobaln.o
ar -crus libbam.a samtools/bgzf.o samtools/kstring.o samtools/bam_aux.o samtools/bam.o samtools/bam_import.o samtools/sam.o samtools/bam_index.o samtools/bam_pileup.o samtools/bam_lpileup.o samtools/bam_md.o samtools/glf.o samtools/razf.o samtools/faidx.o samtools/knetfile.o samtools/bam_sort.o samtools/sam_header.o samtools/bam_reheader.o samtools/kprobaln.o samtools_patch.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/ld.c -o samtools/bcftools/ld.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/kfunc.c -o samtools/bcftools/kfunc.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/index.c -o samtools/bcftools/index.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/fet.c -o samtools/bcftools/fet.o
gcc-4.2 -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/bcf2qcall.c -o samtools/bcftools/bcf2qcall.o
samtools/bcftools/bcf2qcall.c: In function 'bcf_2qcall':
samtools/bcftools/bcf2qcall.c:70: warning: pointer of type 'void *' used in arithmetic
ar -crus libbcf.a samtools/bcftools/bcf.o samtools/bcftools/vcf.o samtools/bcftools/bcfutils.o samtools/bcftools/prob1.o samtools/bcftools/ld.o samtools/bcftools/kfunc.o samtools/bcftools/index.o samtools/bcftools/fet.o samtools/bcftools/bcf2qcall.o samtools_patch.o
mkdir -p /Users/biocbuild/bbs-2.8-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/x86_64
cp Rsamtools.mk /Users/biocbuild/bbs-2.8-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/x86_64
mkdir -p /Users/biocbuild/bbs-2.8-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools
cp samtools/*.h /Users/biocbuild/bbs-2.8-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/
cp samtools/bcftools/*h /Users/biocbuild/bbs-2.8-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools/
mkdir -p /Users/biocbuild/bbs-2.8-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x86_64
cp libbam.a libbcf.a /Users/biocbuild/bbs-2.8-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x86_64
gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o Rsamtools.so Biostrings_stubs.o IRanges_stubs.o R_init_Rsamtools.o as_bam.o bamfile.o bcffile.o encode.o fafile.o io_sam.o samtools_patch.o utilities.o -L. -lbam -lbcf -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/libs/x86_64
* DONE (Rsamtools)
>>>>>>>
>>>>>>> FIXING LINKS FOR Rsamtools.buildbin-libdir/Rsamtools/libs/x86_64/Rsamtools.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" "Rsamtools.buildbin-libdir/Rsamtools/libs/x86_64/Rsamtools.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib" "Rsamtools.buildbin-libdir/Rsamtools/libs/x86_64/Rsamtools.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" "Rsamtools.buildbin-libdir/Rsamtools/libs/x86_64/Rsamtools.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.dylib" "Rsamtools.buildbin-libdir/Rsamtools/libs/x86_64/Rsamtools.so"