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May 5, 2013 04:41
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| (jeans)jeans$ pip install pysam | |
| Downloading/unpacking pysam | |
| Downloading pysam-0.7.4.tar.gz (1.4MB): 1.4MB downloaded | |
| Running setup.py egg_info for package pysam | |
| Downloading http://pypi.python.org/packages/source/d/distribute/distribute-0.6.34.tar.gz | |
| Extracting in /var/folders/vU/vURgXIhFG6O8EVY7ATHbn++++TQ/-Tmp-/tmpE5Lp4T | |
| Now working in /var/folders/vU/vURgXIhFG6O8EVY7ATHbn++++TQ/-Tmp-/tmpE5Lp4T/distribute-0.6.34 | |
| Building a Distribute egg in /Users/abuchanan/.virtualenvs/jeans/build/pysam | |
| /Users/abuchanan/.virtualenvs/jeans/build/pysam/distribute-0.6.34-py2.7.egg | |
| /usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'use_2to3' | |
| warnings.warn(msg) | |
| Downloading/unpacking cython>=0.17 (from pysam) | |
| Downloading Cython-0.19.zip (1.7MB): 1.7MB downloaded | |
| Running setup.py egg_info for package cython | |
| Compiling module Cython.Plex.Scanners ... | |
| Compiling module Cython.Plex.Actions ... | |
| Compiling module Cython.Compiler.Lexicon ... | |
| Compiling module Cython.Compiler.Scanning ... | |
| Compiling module Cython.Compiler.Parsing ... | |
| Compiling module Cython.Compiler.Visitor ... | |
| Compiling module Cython.Compiler.FlowControl ... | |
| Compiling module Cython.Compiler.Code ... | |
| Compiling module Cython.Runtime.refnanny ... | |
| warning: no files found matching '*.pyx' under directory 'Cython/Debugger/Tests' | |
| warning: no files found matching '*.pxd' under directory 'Cython/Debugger/Tests' | |
| warning: no files found matching '*.h' under directory 'Cython/Debugger/Tests' | |
| warning: no files found matching '*.pxd' under directory 'Cython/Utility' | |
| Installing collected packages: pysam, cython | |
| Running setup.py install for pysam | |
| /usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'use_2to3' | |
| warnings.warn(msg) | |
| building 'pysam.csamtools' extension | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c pysam/csamtools.c -o build/temp.macosx-10.6-x86_64-2.7/pysam/csamtools.o | |
| In file included from pysam/csamtools.c:243: | |
| samtools/bam.h:367: warning: function declaration isn’t a prototype | |
| samtools/bam.h:382: warning: function declaration isn’t a prototype | |
| In file included from pysam/csamtools.c:246: | |
| pysam/pysam_util.h:16: warning: function declaration isn’t a prototype | |
| pysam/csamtools.c: In function ‘__pyx_pf_9csamtools_7Samfile_10fetch’: | |
| pysam/csamtools.c:9814: warning: passing argument 7 of ‘bam_fetch’ from incompatible pointer type | |
| pysam/csamtools.c: In function ‘__pyx_pf_9csamtools_7Samfile_11mate’: | |
| pysam/csamtools.c:10254: warning: passing argument 7 of ‘bam_fetch’ from incompatible pointer type | |
| pysam/csamtools.c: In function ‘__pyx_pf_9csamtools_7Samfile_12count’: | |
| pysam/csamtools.c:10730: warning: passing argument 7 of ‘bam_fetch’ from incompatible pointer type | |
| pysam/csamtools.c: In function ‘__pyx_pf_9csamtools_7Samfile_13pileup’: | |
| pysam/csamtools.c:11148: warning: passing argument 7 of ‘bam_fetch’ from incompatible pointer type | |
| pysam/csamtools.c: In function ‘__pyx_f_9csamtools___advance_snpcalls’: | |
| pysam/csamtools.c:17424: warning: implicit declaration of function ‘bam_prob_realn’ | |
| pysam/csamtools.c:17452: warning: implicit declaration of function ‘bam_cap_mapQ’ | |
| pysam/csamtools.c: In function ‘__pyx_pf_9csamtools_20IteratorColumnRegion_1__next__’: | |
| pysam/csamtools.c:18907: warning: passing argument 1 of ‘__pyx_f_9csamtools_makePileupProxy’ from incompatible pointer type | |
| pysam/csamtools.c: In function ‘__pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__’: | |
| pysam/csamtools.c:19134: warning: passing argument 1 of ‘__pyx_f_9csamtools_makePileupProxy’ from incompatible pointer type | |
| pysam/csamtools.c: At top level: | |
| pysam/csamtools.c:2318: warning: ‘__pyx_doc_9csamtools_1genexpr’ defined but not used | |
| pysam/csamtools.c:2456: warning: ‘__pyx_doc_9csamtools_3genexpr’ defined but not used | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c pysam/pysam_util.c -o build/temp.macosx-10.6-x86_64-2.7/pysam/pysam_util.o | |
| In file included from pysam/pysam_util.c:3: | |
| samtools/bam.h:367: warning: function declaration isn’t a prototype | |
| samtools/bam.h:382: warning: function declaration isn’t a prototype | |
| In file included from pysam/pysam_util.c:6: | |
| samtools/bam_endian.h:7: warning: function declaration isn’t a prototype | |
| In file included from pysam/pysam_util.c:8: | |
| pysam/pysam_util.h:16: warning: function declaration isn’t a prototype | |
| pysam/pysam_util.c:28: warning: function declaration isn’t a prototype | |
| pysam/pysam_util.c:63: warning: function declaration isn’t a prototype | |
| pysam/pysam_util.c:64: warning: function declaration isn’t a prototype | |
| pysam/pysam_util.c:97: warning: function declaration isn’t a prototype | |
| pysam/pysam_util.c: In function ‘pysam_pileup_next’: | |
| pysam/pysam_util.c:193: warning: assignment discards qualifiers from pointer target type | |
| pysam/pysam_util.c: At top level: | |
| pysam/pysam_util.c:97: warning: ‘mp_init’ defined but not used | |
| pysam/pysam_util.c:103: warning: ‘mp_destroy’ defined but not used | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bam.c.pysam.o | |
| In file included from samtools/bam.c.pysam.c:7: | |
| samtools/bam.h:367: warning: function declaration isn’t a prototype | |
| samtools/bam.h:382: warning: function declaration isn’t a prototype | |
| In file included from samtools/bam.c.pysam.c:8: | |
| samtools/bam_endian.h:7: warning: function declaration isn’t a prototype | |
| samtools/bam.c.pysam.c:48: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam2bcf.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bam2bcf.c.pysam.o | |
| In file included from samtools/bam2bcf.c.pysam.c:5: | |
| samtools/bam.h:367: warning: function declaration isn’t a prototype | |
| samtools/bam.h:382: warning: function declaration isn’t a prototype | |
| In file included from samtools/bam2bcf.h:6, | |
| from samtools/bam2bcf.c.pysam.c:7: | |
| samtools/bcftools/bcf.h:166: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bam2bcf_indel.c.pysam.o | |
| In file included from samtools/bam2bcf_indel.c.pysam.c:6: | |
| samtools/bam.h:367: warning: function declaration isn’t a prototype | |
| samtools/bam.h:382: warning: function declaration isn’t a prototype | |
| In file included from samtools/bam2bcf.h:6, | |
| from samtools/bam2bcf_indel.c.pysam.c:7: | |
| samtools/bcftools/bcf.h:166: warning: function declaration isn’t a prototype | |
| samtools/bam2bcf_indel.c.pysam.c:11: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam2depth.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bam2depth.c.pysam.o | |
| In file included from samtools/bam2depth.c.pysam.c:13: | |
| samtools/bam.h:367: warning: function declaration isn’t a prototype | |
| samtools/bam.h:382: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_aux.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bam_aux.c.pysam.o | |
| In file included from samtools/bam_aux.c.pysam.c:4: | |
| samtools/bam.h:367: warning: function declaration isn’t a prototype | |
| samtools/bam.h:382: warning: function declaration isn’t a prototype | |
| samtools/bam_aux.c.pysam.c:7: warning: function declaration isn’t a prototype | |
| samtools/bam_aux.c.pysam.c:8: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_cat.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bam_cat.c.pysam.o | |
| In file included from samtools/bam_cat.c.pysam.c:65: | |
| samtools/bam.h:367: warning: function declaration isn’t a prototype | |
| samtools/bam.h:382: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_color.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bam_color.c.pysam.o | |
| In file included from samtools/bam_color.c.pysam.c:4: | |
| samtools/bam.h:367: warning: function declaration isn’t a prototype | |
| samtools/bam.h:382: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_import.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bam_import.c.pysam.o | |
| In file included from samtools/bam_import.c.pysam.c:14: | |
| samtools/bam.h:367: warning: function declaration isn’t a prototype | |
| samtools/bam.h:382: warning: function declaration isn’t a prototype | |
| samtools/bam_import.c.pysam.c:20: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_index.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bam_index.c.pysam.o | |
| In file included from samtools/bam_index.c.pysam.c:5: | |
| samtools/bam.h:367: warning: function declaration isn’t a prototype | |
| samtools/bam.h:382: warning: function declaration isn’t a prototype | |
| In file included from samtools/bam_index.c.pysam.c:8: | |
| samtools/bam_endian.h:7: warning: function declaration isn’t a prototype | |
| samtools/bam_index.c.pysam.c:66: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_lpileup.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bam_lpileup.c.pysam.o | |
| In file included from samtools/bam_lpileup.c.pysam.c:6: | |
| samtools/bam.h:367: warning: function declaration isn’t a prototype | |
| samtools/bam.h:382: warning: function declaration isn’t a prototype | |
| samtools/bam_lpileup.c.pysam.c:26: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_mate.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bam_mate.c.pysam.o | |
| In file included from samtools/bam_mate.c.pysam.c:5: | |
| samtools/bam.h:367: warning: function declaration isn’t a prototype | |
| samtools/bam.h:382: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_md.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bam_md.c.pysam.o | |
| In file included from samtools/sam.h:4, | |
| from samtools/bam_md.c.pysam.c:9: | |
| samtools/bam.h:367: warning: function declaration isn’t a prototype | |
| samtools/bam.h:382: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_pileup.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bam_pileup.c.pysam.o | |
| In file included from samtools/sam.h:4, | |
| from samtools/bam_pileup.c.pysam.c:7: | |
| samtools/bam.h:367: warning: function declaration isn’t a prototype | |
| samtools/bam.h:382: warning: function declaration isn’t a prototype | |
| samtools/bam_pileup.c.pysam.c:30: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_plcmd.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bam_plcmd.c.pysam.o | |
| In file included from samtools/sam.h:4, | |
| from samtools/bam_plcmd.c.pysam.c:9: | |
| samtools/bam.h:367: warning: function declaration isn’t a prototype | |
| samtools/bam.h:382: warning: function declaration isn’t a prototype | |
| In file included from samtools/bam2bcf.h:6, | |
| from samtools/bam_plcmd.c.pysam.c:64: | |
| samtools/bcftools/bcf.h:166: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_reheader.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bam_reheader.c.pysam.o | |
| In file included from samtools/bam_reheader.c.pysam.c:6: | |
| samtools/bam.h:367: warning: function declaration isn’t a prototype | |
| samtools/bam.h:382: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_rmdup.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bam_rmdup.c.pysam.o | |
| In file included from samtools/sam.h:4, | |
| from samtools/bam_rmdup.c.pysam.c:8: | |
| samtools/bam.h:367: warning: function declaration isn’t a prototype | |
| samtools/bam.h:382: warning: function declaration isn’t a prototype | |
| samtools/bam_rmdup.c.pysam.c:13: warning: function declaration isn’t a prototype | |
| samtools/bam_rmdup.c.pysam.c:14: warning: function declaration isn’t a prototype | |
| samtools/bam_rmdup.c.pysam.c:22: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bam_rmdupse.c.pysam.o | |
| In file included from samtools/sam.h:4, | |
| from samtools/bam_rmdupse.c.pysam.c:4: | |
| samtools/bam.h:367: warning: function declaration isn’t a prototype | |
| samtools/bam.h:382: warning: function declaration isn’t a prototype | |
| samtools/bam_rmdupse.c.pysam.c:17: warning: function declaration isn’t a prototype | |
| samtools/bam_rmdupse.c.pysam.c:17: warning: function declaration isn’t a prototype | |
| samtools/bam_rmdupse.c.pysam.c:20: warning: function declaration isn’t a prototype | |
| samtools/bam_rmdupse.c.pysam.c:27: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_sort.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bam_sort.c.pysam.o | |
| In file included from samtools/bam_sort.c.pysam.c:10: | |
| samtools/bam.h:367: warning: function declaration isn’t a prototype | |
| samtools/bam.h:382: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_stat.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bam_stat.c.pysam.o | |
| In file included from samtools/bam_stat.c.pysam.c:5: | |
| samtools/bam.h:367: warning: function declaration isn’t a prototype | |
| samtools/bam.h:382: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_tview.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bam_tview.c.pysam.o | |
| samtools/bam_tview.c.pysam.c:436:2: warning: #warning "No curses library is available; tview is disabled." | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bedidx.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bedidx.c.pysam.o | |
| samtools/bedidx.c.pysam.c:26: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bgzf.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bgzf.c.pysam.o | |
| samtools/bgzf.c.pysam.c:46: warning: function declaration isn’t a prototype | |
| samtools/bgzf.c.pysam.c:143: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/cut_target.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/cut_target.c.pysam.o | |
| In file included from samtools/cut_target.c.pysam.c:6: | |
| samtools/bam.h:367: warning: function declaration isn’t a prototype | |
| samtools/bam.h:382: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/errmod.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/errmod.c.pysam.o | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/faidx.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/faidx.c.pysam.o | |
| samtools/faidx.c.pysam.c:16: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/kaln.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/kaln.c.pysam.o | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/knetfile.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/knetfile.c.pysam.o | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/kprobaln.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/kprobaln.c.pysam.o | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/kstring.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/kstring.c.pysam.o | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/phase.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/phase.c.pysam.o | |
| In file included from samtools/phase.c.pysam.c:9: | |
| samtools/bam.h:367: warning: function declaration isn’t a prototype | |
| samtools/bam.h:382: warning: function declaration isn’t a prototype | |
| samtools/phase.c.pysam.c:47: warning: function declaration isn’t a prototype | |
| samtools/phase.c.pysam.c:48: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/razf.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/razf.c.pysam.o | |
| samtools/razf.c.pysam.c:76: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/sam.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/sam.c.pysam.o | |
| In file included from samtools/sam.h:4, | |
| from samtools/sam.c.pysam.c:6: | |
| samtools/bam.h:367: warning: function declaration isn’t a prototype | |
| samtools/bam.h:382: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/sam_header.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/sam_header.c.pysam.o | |
| samtools/sam_header.c.pysam.c:11: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/sam_view.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/sam_view.c.pysam.o | |
| In file included from samtools/sam.h:4, | |
| from samtools/sam_view.c.pysam.c:9: | |
| samtools/bam.h:367: warning: function declaration isn’t a prototype | |
| samtools/bam.h:382: warning: function declaration isn’t a prototype | |
| samtools/sam_view.c.pysam.c:13: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/sample.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/sample.c.pysam.o | |
| samtools/sample.c.pysam.c:7: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bcftools/bcf.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bcftools/bcf.c.pysam.o | |
| In file included from samtools/bcftools/bcf.c.pysam.c:7: | |
| samtools/bcftools/bcf.h:166: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bcftools/bcf2qcall.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bcftools/bcf2qcall.c.pysam.o | |
| In file included from samtools/bcftools/bcf2qcall.c.pysam.c:7: | |
| samtools/bcftools/bcf.h:166: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bcftools/bcfutils.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bcftools/bcfutils.c.pysam.o | |
| In file included from samtools/bcftools/bcfutils.c.pysam.c:5: | |
| samtools/bcftools/bcf.h:166: warning: function declaration isn’t a prototype | |
| samtools/bcftools/bcfutils.c.pysam.c:8: warning: function declaration isn’t a prototype | |
| samtools/bcftools/bcfutils.c.pysam.c:30: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bcftools/call1.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bcftools/call1.c.pysam.o | |
| In file included from samtools/bcftools/call1.c.pysam.c:8: | |
| samtools/bcftools/bcf.h:166: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bcftools/em.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bcftools/em.c.pysam.o | |
| In file included from samtools/bcftools/em.c.pysam.c:6: | |
| samtools/bcftools/bcf.h:166: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bcftools/fet.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bcftools/fet.c.pysam.o | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bcftools/index.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bcftools/index.c.pysam.o | |
| In file included from samtools/bcftools/index.c.pysam.c:6: | |
| samtools/bam_endian.h:7: warning: function declaration isn’t a prototype | |
| In file included from samtools/bcftools/index.c.pysam.c:8: | |
| samtools/bcftools/bcf.h:166: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bcftools/kfunc.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bcftools/kfunc.c.pysam.o | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bcftools/kmin.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bcftools/kmin.c.pysam.o | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bcftools/mut.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bcftools/mut.c.pysam.o | |
| In file included from samtools/bcftools/mut.c.pysam.c:5: | |
| samtools/bcftools/bcf.h:166: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bcftools/prob1.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bcftools/prob1.c.pysam.o | |
| In file included from samtools/bcftools/prob1.h:4, | |
| from samtools/bcftools/prob1.c.pysam.c:9: | |
| samtools/bcftools/bcf.h:166: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bcftools/vcf.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/bcftools/vcf.c.pysam.o | |
| In file included from samtools/bcftools/vcf.c.pysam.c:7: | |
| samtools/bcftools/bcf.h:166: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/misc/md5.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/misc/md5.c.pysam.o | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/misc/seqtk.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/samtools/misc/seqtk.c.pysam.o | |
| samtools/misc/seqtk.c.pysam.c:21: warning: function declaration isn’t a prototype | |
| samtools/misc/seqtk.c.pysam.c:749: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -bundle -undefined dynamic_lookup -L/usr/local/opt/sqlite/lib -L/usr/local/opt/readline/lib -L/usr/local/lib build/temp.macosx-10.6-x86_64-2.7/pysam/csamtools.o build/temp.macosx-10.6-x86_64-2.7/pysam/pysam_util.o build/temp.macosx-10.6-x86_64-2.7/samtools/bam.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/bam2bcf.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/bam2bcf_indel.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/bam2depth.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/bam_aux.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/bam_cat.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/bam_color.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/bam_import.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/bam_index.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/bam_lpileup.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/bam_mate.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/bam_md.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/bam_pileup.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/bam_plcmd.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/bam_reheader.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/bam_rmdup.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/bam_rmdupse.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/bam_sort.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/bam_stat.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/bam_tview.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/bedidx.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/bgzf.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/cut_target.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/errmod.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/faidx.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/kaln.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/knetfile.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/kprobaln.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/kstring.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/phase.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/razf.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/sam.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/sam_header.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/sam_view.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/sample.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/bcftools/bcf.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/bcftools/bcf2qcall.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/bcftools/bcfutils.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/bcftools/call1.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/bcftools/em.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/bcftools/fet.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/bcftools/index.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/bcftools/kfunc.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/bcftools/kmin.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/bcftools/mut.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/bcftools/prob1.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/bcftools/vcf.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/misc/md5.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/samtools/misc/seqtk.c.pysam.o -lz -o build/lib.macosx-10.6-x86_64-2.7/pysam/csamtools.so | |
| building 'pysam.ctabix' extension | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Itabix -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c pysam/ctabix.c -o build/temp.macosx-10.6-x86_64-2.7/pysam/ctabix.o | |
| pysam/ctabix.c: In function ‘__pyx_pf_5pysam_6ctabix_9Tabixfile_7contigs___get__’: | |
| pysam/ctabix.c:4042: warning: assignment from incompatible pointer type | |
| pysam/ctabix.c: In function ‘__pyx_pf_5pysam_6ctabix_13TabixIterator_4__next__’: | |
| pysam/ctabix.c:4543: warning: assignment discards qualifiers from pointer target type | |
| pysam/ctabix.c: In function ‘__pyx_pf_5pysam_6ctabix_19TabixHeaderIterator_4__next__’: | |
| pysam/ctabix.c:4892: warning: assignment discards qualifiers from pointer target type | |
| pysam/ctabix.c: In function ‘__pyx_pf_5pysam_6ctabix_19TabixIteratorParsed_4__next__’: | |
| pysam/ctabix.c:5824: warning: assignment discards qualifiers from pointer target type | |
| pysam/ctabix.c: In function ‘__pyx_f_5pysam_6ctabix_22tabix_inplace_iterator___cnext__’: | |
| pysam/ctabix.c:7645: warning: implicit declaration of function ‘getline’ | |
| pysam/ctabix.c: At top level: | |
| pysam/ctabix.c:1518: warning: ‘__pyx_f_5pysam_6ctabix_from_string_and_size’ defined but not used | |
| pysam/ctabix.c:1988: warning: ‘__pyx_f_5pysam_6ctabix__force_str’ defined but not used | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Itabix -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c pysam/tabix_util.c -o build/temp.macosx-10.6-x86_64-2.7/pysam/tabix_util.o | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Itabix -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c tabix/bedidx.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/tabix/bedidx.c.pysam.o | |
| tabix/bedidx.c.pysam.c:22: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Itabix -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c tabix/bgzf.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/tabix/bgzf.c.pysam.o | |
| tabix/bgzf.c.pysam.c:105: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Itabix -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c tabix/bgzip.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/tabix/bgzip.c.pysam.o | |
| tabix/bgzip.c.pysam.c:39: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Itabix -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c tabix/index.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/tabix/index.c.pysam.o | |
| In file included from tabix/index.c.pysam.c:9: | |
| tabix/bam_endian.h:7: warning: function declaration isn’t a prototype | |
| tabix/index.c.pysam.c:36: warning: function declaration isn’t a prototype | |
| tabix/index.c.pysam.c:37: warning: function declaration isn’t a prototype | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Itabix -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c tabix/knetfile.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/tabix/knetfile.c.pysam.o | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Itabix -Ipysam -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c tabix/kstring.c.pysam.c -o build/temp.macosx-10.6-x86_64-2.7/tabix/kstring.c.pysam.o | |
| /usr/bin/gcc-4.2 -bundle -undefined dynamic_lookup -L/usr/local/opt/sqlite/lib -L/usr/local/opt/readline/lib -L/usr/local/lib build/temp.macosx-10.6-x86_64-2.7/pysam/ctabix.o build/temp.macosx-10.6-x86_64-2.7/pysam/tabix_util.o build/temp.macosx-10.6-x86_64-2.7/tabix/bedidx.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/tabix/bgzf.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/tabix/bgzip.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/tabix/index.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/tabix/knetfile.c.pysam.o build/temp.macosx-10.6-x86_64-2.7/tabix/kstring.c.pysam.o -lz -o build/lib.macosx-10.6-x86_64-2.7/pysam/ctabix.so | |
| building 'pysam.TabProxies' extension | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c pysam/TabProxies.c -o build/temp.macosx-10.6-x86_64-2.7/pysam/TabProxies.o | |
| pysam/TabProxies.c:1168: warning: ‘__pyx_f_10TabProxies_from_string_and_size’ defined but not used | |
| pysam/TabProxies.c:1241: warning: ‘__pyx_f_10TabProxies__my_encodeFilename’ defined but not used | |
| pysam/TabProxies.c:1565: warning: ‘__pyx_f_10TabProxies__charptr_to_str’ defined but not used | |
| pysam/TabProxies.c:1763: warning: ‘__pyx_f_10TabProxies_nextItem’ defined but not used | |
| /usr/bin/gcc-4.2 -bundle -undefined dynamic_lookup -L/usr/local/opt/sqlite/lib -L/usr/local/opt/readline/lib -L/usr/local/lib build/temp.macosx-10.6-x86_64-2.7/pysam/TabProxies.o -lz -o build/lib.macosx-10.6-x86_64-2.7/pysam/TabProxies.so | |
| building 'pysam.cvcf' extension | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Itabix -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c pysam/cvcf.c -o build/temp.macosx-10.6-x86_64-2.7/pysam/cvcf.o | |
| pysam/cvcf.c: In function ‘__pyx_pw_5pysam_4cvcf_3VCF_33parse_data’: | |
| pysam/cvcf.c:14581: warning: ‘__pyx_v_qual’ may be used uninitialized in this function | |
| pysam/cvcf.c:14581: note: ‘__pyx_v_qual’ was declared here | |
| /usr/bin/gcc-4.2 -bundle -undefined dynamic_lookup -L/usr/local/opt/sqlite/lib -L/usr/local/opt/readline/lib -L/usr/local/lib build/temp.macosx-10.6-x86_64-2.7/pysam/cvcf.o -lz -o build/lib.macosx-10.6-x86_64-2.7/pysam/cvcf.so | |
| Running setup.py install for cython | |
| building 'Cython.Plex.Scanners' extension | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c /Users/abuchanan/.virtualenvs/jeans/build/cython/Cython/Plex/Scanners.c -o build/temp.macosx-10.6-x86_64-2.7/Users/abuchanan/.virtualenvs/jeans/build/cython/Cython/Plex/Scanners.o | |
| /usr/bin/gcc-4.2 -bundle -undefined dynamic_lookup -L/usr/local/opt/sqlite/lib -L/usr/local/opt/readline/lib -L/usr/local/lib build/temp.macosx-10.6-x86_64-2.7/Users/abuchanan/.virtualenvs/jeans/build/cython/Cython/Plex/Scanners.o -o build/lib.macosx-10.6-x86_64-2.7/Cython/Plex/Scanners.so | |
| building 'Cython.Plex.Actions' extension | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c /Users/abuchanan/.virtualenvs/jeans/build/cython/Cython/Plex/Actions.c -o build/temp.macosx-10.6-x86_64-2.7/Users/abuchanan/.virtualenvs/jeans/build/cython/Cython/Plex/Actions.o | |
| /usr/bin/gcc-4.2 -bundle -undefined dynamic_lookup -L/usr/local/opt/sqlite/lib -L/usr/local/opt/readline/lib -L/usr/local/lib build/temp.macosx-10.6-x86_64-2.7/Users/abuchanan/.virtualenvs/jeans/build/cython/Cython/Plex/Actions.o -o build/lib.macosx-10.6-x86_64-2.7/Cython/Plex/Actions.so | |
| building 'Cython.Compiler.Lexicon' extension | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c /Users/abuchanan/.virtualenvs/jeans/build/cython/Cython/Compiler/Lexicon.c -o build/temp.macosx-10.6-x86_64-2.7/Users/abuchanan/.virtualenvs/jeans/build/cython/Cython/Compiler/Lexicon.o | |
| /usr/bin/gcc-4.2 -bundle -undefined dynamic_lookup -L/usr/local/opt/sqlite/lib -L/usr/local/opt/readline/lib -L/usr/local/lib build/temp.macosx-10.6-x86_64-2.7/Users/abuchanan/.virtualenvs/jeans/build/cython/Cython/Compiler/Lexicon.o -o build/lib.macosx-10.6-x86_64-2.7/Cython/Compiler/Lexicon.so | |
| building 'Cython.Compiler.Scanning' extension | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c /Users/abuchanan/.virtualenvs/jeans/build/cython/Cython/Compiler/Scanning.c -o build/temp.macosx-10.6-x86_64-2.7/Users/abuchanan/.virtualenvs/jeans/build/cython/Cython/Compiler/Scanning.o | |
| /usr/bin/gcc-4.2 -bundle -undefined dynamic_lookup -L/usr/local/opt/sqlite/lib -L/usr/local/opt/readline/lib -L/usr/local/lib build/temp.macosx-10.6-x86_64-2.7/Users/abuchanan/.virtualenvs/jeans/build/cython/Cython/Compiler/Scanning.o -o build/lib.macosx-10.6-x86_64-2.7/Cython/Compiler/Scanning.so | |
| building 'Cython.Compiler.Parsing' extension | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c /Users/abuchanan/.virtualenvs/jeans/build/cython/Cython/Compiler/Parsing.c -o build/temp.macosx-10.6-x86_64-2.7/Users/abuchanan/.virtualenvs/jeans/build/cython/Cython/Compiler/Parsing.o | |
| /usr/bin/gcc-4.2 -bundle -undefined dynamic_lookup -L/usr/local/opt/sqlite/lib -L/usr/local/opt/readline/lib -L/usr/local/lib build/temp.macosx-10.6-x86_64-2.7/Users/abuchanan/.virtualenvs/jeans/build/cython/Cython/Compiler/Parsing.o -o build/lib.macosx-10.6-x86_64-2.7/Cython/Compiler/Parsing.so | |
| building 'Cython.Compiler.Visitor' extension | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c /Users/abuchanan/.virtualenvs/jeans/build/cython/Cython/Compiler/Visitor.c -o build/temp.macosx-10.6-x86_64-2.7/Users/abuchanan/.virtualenvs/jeans/build/cython/Cython/Compiler/Visitor.o | |
| /usr/bin/gcc-4.2 -bundle -undefined dynamic_lookup -L/usr/local/opt/sqlite/lib -L/usr/local/opt/readline/lib -L/usr/local/lib build/temp.macosx-10.6-x86_64-2.7/Users/abuchanan/.virtualenvs/jeans/build/cython/Cython/Compiler/Visitor.o -o build/lib.macosx-10.6-x86_64-2.7/Cython/Compiler/Visitor.so | |
| building 'Cython.Compiler.FlowControl' extension | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c /Users/abuchanan/.virtualenvs/jeans/build/cython/Cython/Compiler/FlowControl.c -o build/temp.macosx-10.6-x86_64-2.7/Users/abuchanan/.virtualenvs/jeans/build/cython/Cython/Compiler/FlowControl.o | |
| /usr/bin/gcc-4.2 -bundle -undefined dynamic_lookup -L/usr/local/opt/sqlite/lib -L/usr/local/opt/readline/lib -L/usr/local/lib build/temp.macosx-10.6-x86_64-2.7/Users/abuchanan/.virtualenvs/jeans/build/cython/Cython/Compiler/FlowControl.o -o build/lib.macosx-10.6-x86_64-2.7/Cython/Compiler/FlowControl.so | |
| building 'Cython.Compiler.Code' extension | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c /Users/abuchanan/.virtualenvs/jeans/build/cython/Cython/Compiler/Code.c -o build/temp.macosx-10.6-x86_64-2.7/Users/abuchanan/.virtualenvs/jeans/build/cython/Cython/Compiler/Code.o | |
| /usr/bin/gcc-4.2 -bundle -undefined dynamic_lookup -L/usr/local/opt/sqlite/lib -L/usr/local/opt/readline/lib -L/usr/local/lib build/temp.macosx-10.6-x86_64-2.7/Users/abuchanan/.virtualenvs/jeans/build/cython/Cython/Compiler/Code.o -o build/lib.macosx-10.6-x86_64-2.7/Cython/Compiler/Code.so | |
| building 'Cython.Runtime.refnanny' extension | |
| /usr/bin/gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -Os -pipe -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c /Users/abuchanan/.virtualenvs/jeans/build/cython/Cython/Runtime/refnanny.c -o build/temp.macosx-10.6-x86_64-2.7/Users/abuchanan/.virtualenvs/jeans/build/cython/Cython/Runtime/refnanny.o | |
| /usr/bin/gcc-4.2 -bundle -undefined dynamic_lookup -L/usr/local/opt/sqlite/lib -L/usr/local/opt/readline/lib -L/usr/local/lib build/temp.macosx-10.6-x86_64-2.7/Users/abuchanan/.virtualenvs/jeans/build/cython/Cython/Runtime/refnanny.o -o build/lib.macosx-10.6-x86_64-2.7/Cython/Runtime/refnanny.so | |
| changing mode of build/scripts-2.7/cygdb from 644 to 755 | |
| warning: no files found matching '*.pyx' under directory 'Cython/Debugger/Tests' | |
| warning: no files found matching '*.pxd' under directory 'Cython/Debugger/Tests' | |
| warning: no files found matching '*.h' under directory 'Cython/Debugger/Tests' | |
| warning: no files found matching '*.pxd' under directory 'Cython/Utility' | |
| changing mode of /Users/abuchanan/.virtualenvs/jeans/bin/cygdb to 755 | |
| Installing cython script to /Users/abuchanan/.virtualenvs/jeans/bin | |
| Successfully installed pysam cython | |
| Cleaning up... | |
| (jeans)jeans$ ls | |
| count_gene_hits.py test.sam | |
| (jeans)jeans$ python | |
| Python 2.7.3 (default, Mar 29 2013, 13:47:09) | |
| [GCC 4.2.1 (Apple Inc. build 5664)] on darwin | |
| Type "help", "copyright", "credits" or "license" for more information. | |
| >>> import pysam | |
| Traceback (most recent call last): | |
| File "<stdin>", line 1, in <module> | |
| File "/Users/abuchanan/.virtualenvs/jeans/lib/python2.7/site-packages/pysam/__init__.py", line 2, in <module> | |
| from pysam.ctabix import * | |
| ImportError: dlopen(/Users/abuchanan/.virtualenvs/jeans/lib/python2.7/site-packages/pysam/ctabix.so, 2): Symbol not found: _getline | |
| Referenced from: /Users/abuchanan/.virtualenvs/jeans/lib/python2.7/site-packages/pysam/ctabix.so | |
| Expected in: flat namespace | |
| in /Users/abuchanan/.virtualenvs/jeans/lib/python2.7/site-packages/pysam/ctabix.so |
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