Rsamtools 1.6.3
Bioconductor Package Maintainer
| Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/Rsamtools | | Last Changed Rev: 61391 / Revision: 64395 | | Last Changed Date: 2011-12-15 18:47:14 -0800 (Thu, 15 Dec 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | OK | [ OK ] |
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rsamtools.buildbin-libdir Rsamtools_1.6.3.tar.gz'
>>>>>>>
* installing *source* package 'Rsamtools' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c R_init_Rsamtools.c -o R_init_Rsamtools.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c as_bam.c -o as_bam.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c bamfile.c -o bamfile.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c bcffile.c -o bcffile.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c encode.c -o encode.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c fafile.c -o fafile.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c io_sam.c -o io_sam.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c pileupbam.c -o pileupbam.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools_patch.c -o samtools_patch.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c tabixfile.c -o tabixfile.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c utilities.c -o utilities.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c vcffile.c -o vcffile.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c zip_compression.c -o zip_compression.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bgzf.c -o samtools/bgzf.o
samtools/bgzf.c: In function 'deflate_block':
samtools/bgzf.c:358: warning: pointer of type 'void *' used in arithmetic
samtools/bgzf.c: In function 'inflate_block':
samtools/bgzf.c:375: warning: pointer of type 'void *' used in arithmetic
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/kstring.c -o samtools/kstring.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bam_aux.c -o samtools/bam_aux.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bam.c -o samtools/bam.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bam_import.c -o samtools/bam_import.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/sam.c -o samtools/sam.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bam_index.c -o samtools/bam_index.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bam_pileup.c -o samtools/bam_pileup.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bam_md.c -o samtools/bam_md.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -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 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/faidx.c -o samtools/faidx.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -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 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -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:309: warning: 'bam1_lt' is static but used in inline function '__ks_insertsort_sort' which is not static
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/sam_header.c -o samtools/sam_header.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -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 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -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/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 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o
samtools/bcftools/bcfutils.c: In function 'bcf_gl10':
samtools/bcftools/bcfutils.c:355: warning: pointer of type 'void *' used in arithmetic
samtools/bcftools/bcfutils.c: In function 'bcf_gl10_indel':
samtools/bcftools/bcfutils.c:378: warning: pointer of type 'void *' used in arithmetic
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/kfunc.c -o samtools/bcftools/kfunc.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/index.c -o samtools/bcftools/index.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/fet.c -o samtools/bcftools/fet.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -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/kfunc.o samtools/bcftools/index.o samtools/bcftools/fet.o samtools/bcftools/bcf2qcall.o samtools_patch.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c tabix/index.c -o tabix/index.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c tabix/bedidx.c -o tabix/bedidx.o
ar -crus libtabix.a samtools/bgzf.o samtools/kstring.o samtools/knetfile.o tabix/index.o tabix/bedidx.o samtools_patch.o
mkdir -p "/Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/i386"
cp ../Rsamtools.mk "/Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/i386"
mkdir -p "/Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools"
mkdir -p "/Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix"
cp samtools/*.h "/Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/"
cp samtools/bcftools/*h "/Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools/"
cp tabix/*h "/Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix/"
mkdir -p "/Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386"
cp libbam.a libbcf.a libtabix.a "/Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386"
gcc -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 pileupbam.o samtools_patch.o tabixfile.o utilities.o vcffile.o zip_compression.o /Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386/libbam.a /Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386/libbcf.a /Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/i386/libtabix.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
'Rsamtools-Overview.Rnw'
'Rsamtools-UsingCLibraries.Rnw'
** 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/2.14/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/2.14/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/2.14/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/2.14/Resources/lib/libreadline.dylib" "Rsamtools.buildbin-libdir/Rsamtools/libs/i386/Rsamtools.so"
>>>>>>>
>>>>>>> INSTALLATION OF ppc LIBS WITH 'R_ARCH=/ppc R CMD INSTALL --preclean --no-multiarch --no-test-load --library=Rsamtools.buildbin-libdir --libs-only Rsamtools_1.6.3.tar.gz'
>>>>>>>
* installing *source* package 'Rsamtools' ...
** libs
*** arch - ppc
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c R_init_Rsamtools.c -o R_init_Rsamtools.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c as_bam.c -o as_bam.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c bamfile.c -o bamfile.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c bcffile.c -o bcffile.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c encode.c -o encode.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c fafile.c -o fafile.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c io_sam.c -o io_sam.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c pileupbam.c -o pileupbam.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools_patch.c -o samtools_patch.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c tabixfile.c -o tabixfile.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c utilities.c -o utilities.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c vcffile.c -o vcffile.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c zip_compression.c -o zip_compression.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bgzf.c -o samtools/bgzf.o
samtools/bgzf.c: In function 'deflate_block':
samtools/bgzf.c:358: warning: pointer of type 'void *' used in arithmetic
samtools/bgzf.c: In function 'inflate_block':
samtools/bgzf.c:375: warning: pointer of type 'void *' used in arithmetic
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/kstring.c -o samtools/kstring.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bam_aux.c -o samtools/bam_aux.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bam.c -o samtools/bam.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bam_import.c -o samtools/bam_import.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/sam.c -o samtools/sam.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bam_index.c -o samtools/bam_index.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bam_pileup.c -o samtools/bam_pileup.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bam_md.c -o samtools/bam_md.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -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 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/faidx.c -o samtools/faidx.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -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 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -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:309: warning: 'bam1_lt' is static but used in inline function '__ks_insertsort_sort' which is not static
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/sam_header.c -o samtools/sam_header.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -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 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -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/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 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o
samtools/bcftools/bcfutils.c: In function 'bcf_gl10':
samtools/bcftools/bcfutils.c:355: warning: pointer of type 'void *' used in arithmetic
samtools/bcftools/bcfutils.c: In function 'bcf_gl10_indel':
samtools/bcftools/bcfutils.c:378: warning: pointer of type 'void *' used in arithmetic
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/kfunc.c -o samtools/bcftools/kfunc.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/index.c -o samtools/bcftools/index.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/fet.c -o samtools/bcftools/fet.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -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/kfunc.o samtools/bcftools/index.o samtools/bcftools/fet.o samtools/bcftools/bcf2qcall.o samtools_patch.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c tabix/index.c -o tabix/index.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c tabix/bedidx.c -o tabix/bedidx.o
ar -crus libtabix.a samtools/bgzf.o samtools/kstring.o samtools/knetfile.o tabix/index.o tabix/bedidx.o samtools_patch.o
mkdir -p "/Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/ppc"
cp ../Rsamtools.mk "/Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/ppc"
mkdir -p "/Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools"
mkdir -p "/Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix"
cp samtools/*.h "/Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/"
cp samtools/bcftools/*h "/Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools/"
cp tabix/*h "/Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix/"
mkdir -p "/Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/ppc"
cp libbam.a libbcf.a libtabix.a "/Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/ppc"
gcc -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 pileupbam.o samtools_patch.o tabixfile.o utilities.o vcffile.o zip_compression.o /Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/ppc/libbam.a /Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/ppc/libbcf.a /Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/ppc/libtabix.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-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/2.14/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/2.14/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/2.14/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/2.14/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 --no-multiarch --no-test-load --library=Rsamtools.buildbin-libdir --libs-only Rsamtools_1.6.3.tar.gz'
>>>>>>>
* installing *source* package 'Rsamtools' ...
** 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 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c R_init_Rsamtools.c -o R_init_Rsamtools.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c as_bam.c -o as_bam.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c bamfile.c -o bamfile.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c bcffile.c -o bcffile.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c encode.c -o encode.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c fafile.c -o fafile.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c io_sam.c -o io_sam.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c pileupbam.c -o pileupbam.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools_patch.c -o samtools_patch.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c tabixfile.c -o tabixfile.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c utilities.c -o utilities.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c vcffile.c -o vcffile.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c zip_compression.c -o zip_compression.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bgzf.c -o samtools/bgzf.o
samtools/bgzf.c: In function 'deflate_block':
samtools/bgzf.c:358: warning: pointer of type 'void *' used in arithmetic
samtools/bgzf.c: In function 'inflate_block':
samtools/bgzf.c:375: warning: pointer of type 'void *' used in arithmetic
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/kstring.c -o samtools/kstring.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bam_aux.c -o samtools/bam_aux.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bam.c -o samtools/bam.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bam_import.c -o samtools/bam_import.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/sam.c -o samtools/sam.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bam_index.c -o samtools/bam_index.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bam_pileup.c -o samtools/bam_pileup.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bam_lpileup.c -o samtools/bam_lpileup.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bam_md.c -o samtools/bam_md.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -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 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/faidx.c -o samtools/faidx.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -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 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -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:309: warning: 'bam1_lt' is static but used in inline function '__ks_insertsort_sort' which is not static
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/sam_header.c -o samtools/sam_header.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -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 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -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/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 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/bcf.c -o samtools/bcftools/bcf.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o
samtools/bcftools/bcfutils.c: In function 'bcf_gl10':
samtools/bcftools/bcfutils.c:355: warning: pointer of type 'void *' used in arithmetic
samtools/bcftools/bcfutils.c: In function 'bcf_gl10_indel':
samtools/bcftools/bcfutils.c:378: warning: pointer of type 'void *' used in arithmetic
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/prob1.c -o samtools/bcftools/prob1.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/kfunc.c -o samtools/bcftools/kfunc.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/index.c -o samtools/bcftools/index.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c samtools/bcftools/fet.c -o samtools/bcftools/fet.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -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/kfunc.o samtools/bcftools/index.o samtools/bcftools/fet.o samtools/bcftools/bcf2qcall.o samtools_patch.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c tabix/index.c -o tabix/index.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 -I./tabix -fPIC -g -O2 -Wall -pedantic -c tabix/bedidx.c -o tabix/bedidx.o
ar -crus libtabix.a samtools/bgzf.o samtools/kstring.o samtools/knetfile.o tabix/index.o tabix/bedidx.o samtools_patch.o
mkdir -p "/Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/x86_64"
cp ../Rsamtools.mk "/Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usretc/x86_64"
mkdir -p "/Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools"
mkdir -p "/Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix"
cp samtools/*.h "/Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/"
cp samtools/bcftools/*h "/Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/samtools/bcftools/"
cp tabix/*h "/Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/include/tabix/"
mkdir -p "/Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x86_64"
cp libbam.a libbcf.a libtabix.a "/Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x86_64"
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 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 pileupbam.o samtools_patch.o tabixfile.o utilities.o vcffile.o zip_compression.o /Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x86_64/libbam.a /Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x86_64/libbcf.a /Users/biocbuild/bbs-2.9-bioc/meat/Rsamtools.buildbin-libdir/Rsamtools/usrlib/x86_64/libtabix.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-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/2.14/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/2.14/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/2.14/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/2.14/Resources/lib/libreadline.dylib" "Rsamtools.buildbin-libdir/Rsamtools/libs/x86_64/Rsamtools.so"
tar: Rsamtools/R/Rsamtools.rdb: file changed as we read it