Created
December 9, 2014 15:37
-
-
Save pashields/f7936684c22f9e7a235a to your computer and use it in GitHub Desktop.
ga4gh server install
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| (2.7)λ pashields server → λ git setuppy-fixmes → python setup.py sdist | |
| running sdist | |
| running egg_info | |
| creating ga4gh.egg-info | |
| writing requirements to ga4gh.egg-info/requires.txt | |
| writing ga4gh.egg-info/PKG-INFO | |
| writing top-level names to ga4gh.egg-info/top_level.txt | |
| writing dependency_links to ga4gh.egg-info/dependency_links.txt | |
| writing entry points to ga4gh.egg-info/entry_points.txt | |
| writing manifest file 'ga4gh.egg-info/SOURCES.txt' | |
| reading manifest file 'ga4gh.egg-info/SOURCES.txt' | |
| reading manifest template 'MANIFEST.in' | |
| writing manifest file 'ga4gh.egg-info/SOURCES.txt' | |
| running check | |
| creating ga4gh-0.5.0 | |
| creating ga4gh-0.5.0/ga4gh | |
| creating ga4gh-0.5.0/ga4gh.egg-info | |
| making hard links in ga4gh-0.5.0... | |
| hard linking LICENSE -> ga4gh-0.5.0 | |
| hard linking MANIFEST.in -> ga4gh-0.5.0 | |
| hard linking README.rst -> ga4gh-0.5.0 | |
| hard linking README.txt -> ga4gh-0.5.0 | |
| hard linking ez_setup.py -> ga4gh-0.5.0 | |
| hard linking setup.py -> ga4gh-0.5.0 | |
| hard linking ga4gh/__init__.py -> ga4gh-0.5.0/ga4gh | |
| hard linking ga4gh/cli.py -> ga4gh-0.5.0/ga4gh | |
| hard linking ga4gh/client.py -> ga4gh-0.5.0/ga4gh | |
| hard linking ga4gh/protocol.py -> ga4gh-0.5.0/ga4gh | |
| hard linking ga4gh/server.py -> ga4gh-0.5.0/ga4gh | |
| hard linking ga4gh.egg-info/PKG-INFO -> ga4gh-0.5.0/ga4gh.egg-info | |
| hard linking ga4gh.egg-info/SOURCES.txt -> ga4gh-0.5.0/ga4gh.egg-info | |
| hard linking ga4gh.egg-info/dependency_links.txt -> ga4gh-0.5.0/ga4gh.egg-info | |
| hard linking ga4gh.egg-info/entry_points.txt -> ga4gh-0.5.0/ga4gh.egg-info | |
| hard linking ga4gh.egg-info/requires.txt -> ga4gh-0.5.0/ga4gh.egg-info | |
| hard linking ga4gh.egg-info/top_level.txt -> ga4gh-0.5.0/ga4gh.egg-info | |
| Writing ga4gh-0.5.0/setup.cfg | |
| creating dist | |
| Creating tar archive | |
| removing 'ga4gh-0.5.0' (and everything under it) | |
| (2.7)λ pashields server → λ git setuppy-fixmes* → | |
| λ pashields ~ → mkvirtualenv -p /usr/bin/python2.7 ga4gh-pip-install | |
| Running virtualenv with interpreter /usr/bin/python2.7 | |
| New python executable in ga4gh-pip-install/bin/python2.7 | |
| Also creating executable in ga4gh-pip-install/bin/python | |
| Installing setuptools, pip...done. | |
| (ga4gh-pip-install)λ pashields ~ → pip install sandboxes/server/dist/ga4gh-0.5.0.tar.gz | |
| Unpacking ./sandboxes/server/dist/ga4gh-0.5.0.tar.gz | |
| Running setup.py (path:/tmp/pip-ERfkUB-build/setup.py) egg_info for package from file:///usr/local/google/home/pashields/sandboxes/server/dist/ga4gh-0.5.0.tar.gz | |
| The required version of setuptools (>=5.4.1) is not available, | |
| and can't be installed while this script is running. Please | |
| install a more recent version first, using | |
| 'easy_install -U setuptools'. | |
| (Currently using setuptools 3.6 (/usr/local/google/home/pashields/Envs/ga4gh-pip-install/lib/python2.7/site-packages)) | |
| Complete output from command python setup.py egg_info: | |
| The required version of setuptools (>=5.4.1) is not available, | |
| and can't be installed while this script is running. Please | |
| install a more recent version first, using | |
| 'easy_install -U setuptools'. | |
| (Currently using setuptools 3.6 (/usr/local/google/home/pashields/Envs/ga4gh-pip-install/lib/python2.7/site-packages)) | |
| ---------------------------------------- | |
| Cleaning up... | |
| Command python setup.py egg_info failed with error code 2 in /tmp/pip-ERfkUB-build | |
| Storing debug log for failure in /usr/local/google/home/pashields/.pip/pip.log | |
| (ga4gh-pip-install)λ pashields ~ → easy_install -U setuptools | |
| Searching for setuptools | |
| Reading https://pypi.python.org/simple/setuptools/ | |
| Best match: setuptools 7.0 | |
| Downloading https://pypi.python.org/packages/source/s/setuptools/setuptools-7.0.zip#md5=5771b7ab257e70603e620b2313d1e971 | |
| Processing setuptools-7.0.zip | |
| Writing /tmp/easy_install-jIOoLI/setuptools-7.0/setup.cfg | |
| Running setuptools-7.0/setup.py -q bdist_egg --dist-dir /tmp/easy_install-jIOoLI/setuptools-7.0/egg-dist-tmp-mKcICG | |
| Adding setuptools 7.0 to easy-install.pth file | |
| Installing easy_install script to /usr/local/google/home/pashields/Envs/ga4gh-pip-install/bin | |
| Installing easy_install-2.7 script to /usr/local/google/home/pashields/Envs/ga4gh-pip-install/bin | |
| Installed /usr/local/google/home/pashields/Envs/ga4gh-pip-install/lib/python2.7/site-packages/setuptools-7.0-py2.7.egg | |
| Processing dependencies for setuptools | |
| Finished processing dependencies for setuptools | |
| (ga4gh-pip-install)λ pashields ~ → pip install sandboxes/server/dist/ga4gh-0.5.0.tar.gz | |
| Unpacking ./sandboxes/server/dist/ga4gh-0.5.0.tar.gz | |
| Running setup.py (path:/tmp/pip-7Zlm3n-build/setup.py) egg_info for package from file:///usr/local/google/home/pashields/sandboxes/server/dist/ga4gh-0.5.0.tar.gz | |
| Downloading/unpacking werkzeug (from ga4gh==0.5.0) | |
| Downloading Werkzeug-0.9.6.tar.gz (1.1MB): 1.1MB downloaded | |
| Running setup.py (path:/usr/local/google/home/pashields/Envs/ga4gh-pip-install/build/werkzeug/setup.py) egg_info for package werkzeug | |
| warning: no files found matching '*' under directory 'werkzeug/debug/templates' | |
| warning: no files found matching '*' under directory 'tests' | |
| warning: no previously-included files matching '*.pyc' found under directory 'docs' | |
| warning: no previously-included files matching '*.pyo' found under directory 'docs' | |
| warning: no previously-included files matching '*.pyc' found under directory 'tests' | |
| warning: no previously-included files matching '*.pyo' found under directory 'tests' | |
| warning: no previously-included files matching '*.pyc' found under directory 'examples' | |
| warning: no previously-included files matching '*.pyo' found under directory 'examples' | |
| no previously-included directories found matching 'docs/_build' | |
| Downloading/unpacking wormtable (from ga4gh==0.5.0) | |
| Downloading wormtable-0.1.2.tar.gz (90kB): 90kB downloaded | |
| Running setup.py (path:/usr/local/google/home/pashields/Envs/ga4gh-pip-install/build/wormtable/setup.py) egg_info for package wormtable | |
| Downloading/unpacking avro (from ga4gh==0.5.0) | |
| Downloading avro-1.7.7.tar.gz | |
| Running setup.py (path:/usr/local/google/home/pashields/Envs/ga4gh-pip-install/build/avro/setup.py) egg_info for package avro | |
| Downloading/unpacking pysam (from ga4gh==0.5.0) | |
| Downloading pysam-0.8.1.tar.gz (1.2MB): 1.2MB downloaded | |
| Running setup.py (path:/usr/local/google/home/pashields/Envs/ga4gh-pip-install/build/pysam/setup.py) egg_info for package pysam | |
| package init file 'htslib/__init__.py' not found (or not a regular file) | |
| package init file 'htslib/htslib/__init__.py' not found (or not a regular file) | |
| package init file 'samtools/__init__.py' not found (or not a regular file) | |
| package init file 'samtools/win32/__init__.py' not found (or not a regular file) | |
| warning: no files found matching 'tests/pysam_data' | |
| warning: no files found matching 'tests/tabix_data' | |
| Downloading/unpacking requests (from ga4gh==0.5.0) | |
| Downloading requests-2.5.0-py2.py3-none-any.whl (464kB): 464kB downloaded | |
| Installing collected packages: werkzeug, wormtable, avro, pysam, requests, ga4gh | |
| Running setup.py install for werkzeug | |
| warning: no files found matching '*' under directory 'werkzeug/debug/templates' | |
| warning: no files found matching '*' under directory 'tests' | |
| warning: no previously-included files matching '*.pyc' found under directory 'docs' | |
| warning: no previously-included files matching '*.pyo' found under directory 'docs' | |
| warning: no previously-included files matching '*.pyc' found under directory 'tests' | |
| warning: no previously-included files matching '*.pyo' found under directory 'tests' | |
| warning: no previously-included files matching '*.pyc' found under directory 'examples' | |
| warning: no previously-included files matching '*.pyo' found under directory 'examples' | |
| no previously-included directories found matching 'docs/_build' | |
| Running setup.py install for wormtable | |
| building '_wormtable' extension | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/include/python2.7 -c _wormtablemodule.c -o build/temp.linux-x86_64-2.7/_wormtablemodule.o | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/include/python2.7 -c halffloat.c -o build/temp.linux-x86_64-2.7/halffloat.o | |
| x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/_wormtablemodule.o build/temp.linux-x86_64-2.7/halffloat.o -ldb -o build/lib.linux-x86_64-2.7/_wormtable.so | |
| changing mode of build/scripts-2.7/vcf2wt from 640 to 755 | |
| changing mode of build/scripts-2.7/wtadmin from 640 to 755 | |
| changing mode of build/scripts-2.7/gtf2wt from 640 to 755 | |
| changing mode of /usr/local/google/home/pashields/Envs/ga4gh-pip-install/bin/gtf2wt to 755 | |
| changing mode of /usr/local/google/home/pashields/Envs/ga4gh-pip-install/bin/vcf2wt to 755 | |
| changing mode of /usr/local/google/home/pashields/Envs/ga4gh-pip-install/bin/wtadmin to 755 | |
| Running setup.py install for avro | |
| changing mode of build/scripts-2.7/avro from 640 to 755 | |
| changing mode of /usr/local/google/home/pashields/Envs/ga4gh-pip-install/bin/avro to 755 | |
| Running setup.py install for pysam | |
| package init file 'htslib/__init__.py' not found (or not a regular file) | |
| package init file 'htslib/htslib/__init__.py' not found (or not a regular file) | |
| package init file 'samtools/__init__.py' not found (or not a regular file) | |
| package init file 'samtools/win32/__init__.py' not found (or not a regular file) | |
| building 'pysam.csamtools' extension | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c pysam/csamtools.c -o build/temp.linux-x86_64-2.7/pysam/csamtools.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c pysam/pysam_util.c -o build/temp.linux-x86_64-2.7/pysam/pysam_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| In file included from pysam/pysam_util.c:4:0: | |
| samtools/bam_endian.h:30:19: warning: function declaration isn’t a prototype [-Wstrict-prototypes] | |
| static inline int bam_is_big_endian() | |
| ^ | |
| pysam/pysam_util.c:40:13: warning: function declaration isn’t a prototype [-Wstrict-prototypes] | |
| const char *samtools_version() | |
| ^ | |
| pysam/pysam_util.c: In function ‘samtools_version’: | |
| pysam/pysam_util.c:42:1: warning: control reaches end of non-void function [-Wreturn-type] | |
| } | |
| ^ | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/bam_import.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_import.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/stats_isize.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/padding.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/padding.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/bam_md.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_md.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/errmod.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/errmod.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/bedcov.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bedcov.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam2bcf.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/faidx.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/faidx.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/bam_color.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_color.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/sam.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/sam.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/sam_view.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/sam_view.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_stat.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_lpileup.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_reheader.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| samtools/bam_reheader.c.pysam.c: In function ‘bam_reheader’: | |
| samtools/bam_reheader.c.pysam.c:38:19: warning: variable ‘old’ set but not used [-Wunused-but-set-variable] | |
| bam_header_t *old; | |
| ^ | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_flags.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_plbuf.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bamshuf.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/cut_target.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/cut_target.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/bam_split.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_split.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/bam_index.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_index.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/kprobaln.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/kprobaln.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| samtools/kprobaln.c.pysam.c: In function ‘kpa_glocal’: | |
| samtools/kprobaln.c.pysam.c:80:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable] | |
| int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr; | |
| ^ | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/sam_header.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/sam_header.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_rmdupse.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_rmdup.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/kaln.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/kaln.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/bam_tview_curses.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_tview_curses.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| samtools/bam_tview_curses.c.pysam.c:324:2: warning: #warning "No curses library is available; tview with curses is disabled." [-Wcpp] | |
| #warning "No curses library is available; tview with curses is disabled." | |
| ^ | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam2depth.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/stats.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/stats.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/bam_tview.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_tview.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/phase.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/phase.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_sort.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_cat.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/bedidx.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bedidx.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/bam.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_mate.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/sample.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/sample.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_aux.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam2bcf_indel.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_plcmd.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/bam_tview_html.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_tview_html.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/test/test.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/test/test.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/misc/md5.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/misc/md5.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c samtools/misc/ace2sam.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/misc/ace2sam.c.pysam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/kfunc.c -o build/temp.linux-x86_64-2.7/htslib/kfunc.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/vcfutils.c -o build/temp.linux-x86_64-2.7/htslib/vcfutils.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/sam.c -o build/temp.linux-x86_64-2.7/htslib/sam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/bgzf.c -o build/temp.linux-x86_64-2.7/htslib/bgzf.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/faidx.c -o build/temp.linux-x86_64-2.7/htslib/faidx.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/knetfile.c -o build/temp.linux-x86_64-2.7/htslib/knetfile.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/hfile_net.c -o build/temp.linux-x86_64-2.7/htslib/hfile_net.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/hts.c -o build/temp.linux-x86_64-2.7/htslib/hts.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/hfile.c -o build/temp.linux-x86_64-2.7/htslib/hfile.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/synced_bcf_reader.c -o build/temp.linux-x86_64-2.7/htslib/synced_bcf_reader.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/kstring.c -o build/temp.linux-x86_64-2.7/htslib/kstring.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/vcf_sweep.c -o build/temp.linux-x86_64-2.7/htslib/vcf_sweep.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/vcf.c -o build/temp.linux-x86_64-2.7/htslib/vcf.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/tbx.c -o build/temp.linux-x86_64-2.7/htslib/tbx.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/sam_header.c -o build/temp.linux-x86_64-2.7/htslib/cram/sam_header.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_encode.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_encode.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| htslib/cram/cram_encode.c: In function ‘process_one_read’: | |
| htslib/cram/cram_encode.c:2167:10: warning: unused variable ‘brg’ [-Wunused-variable] | |
| SAM_RG *brg = sam_hdr_find_rg(fd->header, "UNKNOWN"); | |
| ^ | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/string_alloc.c -o build/temp.linux-x86_64-2.7/htslib/cram/string_alloc.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/thread_pool.c -o build/temp.linux-x86_64-2.7/htslib/cram/thread_pool.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_index.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_index.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| htslib/cram/cram_index.c: In function ‘cram_index_build’: | |
| htslib/cram/cram_index.c:431:23: warning: variable ‘hpos’ set but not used [-Wunused-but-set-variable] | |
| off_t cpos, spos, hpos; | |
| ^ | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/mFILE.c -o build/temp.linux-x86_64-2.7/htslib/cram/mFILE.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_samtools.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_samtools.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/pooled_alloc.c -o build/temp.linux-x86_64-2.7/htslib/cram/pooled_alloc.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/open_trace_file.c -o build/temp.linux-x86_64-2.7/htslib/cram/open_trace_file.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/zfio.c -o build/temp.linux-x86_64-2.7/htslib/cram/zfio.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/files.c -o build/temp.linux-x86_64-2.7/htslib/cram/files.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_decode.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_decode.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_codecs.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_codecs.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/md5.c -o build/temp.linux-x86_64-2.7/htslib/cram/md5.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_io.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_io.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/vlen.c -o build/temp.linux-x86_64-2.7/htslib/cram/vlen.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| htslib/cram/vlen.c: In function ‘vflen’: | |
| htslib/cram/vlen.c:121:9: warning: variable ‘i’ set but not used [-Wunused-but-set-variable] | |
| int i; | |
| ^ | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_stats.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_stats.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/pysam/csamtools.o build/temp.linux-x86_64-2.7/pysam/pysam_util.o build/temp.linux-x86_64-2.7/samtools/bam_import.c.pysam.o build/temp.linux-x86_64-2.7/samtools/stats_isize.c.pysam.o build/temp.linux-x86_64-2.7/samtools/padding.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_md.c.pysam.o build/temp.linux-x86_64-2.7/samtools/errmod.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bedcov.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam2bcf.c.pysam.o build/temp.linux-x86_64-2.7/samtools/faidx.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_color.c.pysam.o build/temp.linux-x86_64-2.7/samtools/sam.c.pysam.o build/temp.linux-x86_64-2.7/samtools/sam_view.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_stat.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_lpileup.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_reheader.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_flags.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_plbuf.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bamshuf.c.pysam.o build/temp.linux-x86_64-2.7/samtools/cut_target.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_split.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_index.c.pysam.o build/temp.linux-x86_64-2.7/samtools/kprobaln.c.pysam.o build/temp.linux-x86_64-2.7/samtools/sam_header.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_rmdupse.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_rmdup.c.pysam.o build/temp.linux-x86_64-2.7/samtools/kaln.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_tview_curses.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam2depth.c.pysam.o build/temp.linux-x86_64-2.7/samtools/stats.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_tview.c.pysam.o build/temp.linux-x86_64-2.7/samtools/phase.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_sort.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_cat.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bedidx.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_mate.c.pysam.o build/temp.linux-x86_64-2.7/samtools/sample.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_aux.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam2bcf_indel.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_tview_html.c.pysam.o build/temp.linux-x86_64-2.7/samtools/test/test.c.pysam.o build/temp.linux-x86_64-2.7/samtools/misc/md5.c.pysam.o build/temp.linux-x86_64-2.7/samtools/misc/ace2sam.c.pysam.o build/temp.linux-x86_64-2.7/htslib/kfunc.o build/temp.linux-x86_64-2.7/htslib/vcfutils.o build/temp.linux-x86_64-2.7/htslib/sam.o build/temp.linux-x86_64-2.7/htslib/bgzf.o build/temp.linux-x86_64-2.7/htslib/faidx.o build/temp.linux-x86_64-2.7/htslib/knetfile.o build/temp.linux-x86_64-2.7/htslib/hfile_net.o build/temp.linux-x86_64-2.7/htslib/hts.o build/temp.linux-x86_64-2.7/htslib/hfile.o build/temp.linux-x86_64-2.7/htslib/synced_bcf_reader.o build/temp.linux-x86_64-2.7/htslib/kstring.o build/temp.linux-x86_64-2.7/htslib/vcf_sweep.o build/temp.linux-x86_64-2.7/htslib/vcf.o build/temp.linux-x86_64-2.7/htslib/tbx.o build/temp.linux-x86_64-2.7/htslib/cram/sam_header.o build/temp.linux-x86_64-2.7/htslib/cram/cram_encode.o build/temp.linux-x86_64-2.7/htslib/cram/string_alloc.o build/temp.linux-x86_64-2.7/htslib/cram/thread_pool.o build/temp.linux-x86_64-2.7/htslib/cram/cram_index.o build/temp.linux-x86_64-2.7/htslib/cram/mFILE.o build/temp.linux-x86_64-2.7/htslib/cram/cram_samtools.o build/temp.linux-x86_64-2.7/htslib/cram/pooled_alloc.o build/temp.linux-x86_64-2.7/htslib/cram/open_trace_file.o build/temp.linux-x86_64-2.7/htslib/cram/zfio.o build/temp.linux-x86_64-2.7/htslib/cram/files.o build/temp.linux-x86_64-2.7/htslib/cram/cram_decode.o build/temp.linux-x86_64-2.7/htslib/cram/cram_codecs.o build/temp.linux-x86_64-2.7/htslib/cram/md5.o build/temp.linux-x86_64-2.7/htslib/cram/cram_io.o build/temp.linux-x86_64-2.7/htslib/cram/vlen.o build/temp.linux-x86_64-2.7/htslib/cram/cram_stats.o -lz -o build/lib.linux-x86_64-2.7/pysam/csamtools.so | |
| building 'pysam.libchtslib' extension | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c pysam/chtslib.c -o build/temp.linux-x86_64-2.7/pysam/chtslib.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| pysam/chtslib.c:911:18: warning: ‘__pyx_f_5pysam_10libchtslib_from_string_and_size’ defined but not used [-Wunused-function] | |
| static PyObject *__pyx_f_5pysam_10libchtslib_from_string_and_size(char *__pyx_v_s, size_t __pyx_v_length) { | |
| ^ | |
| pysam/chtslib.c:992:18: warning: ‘__pyx_f_5pysam_10libchtslib__encodeFilename’ defined but not used [-Wunused-function] | |
| static PyObject *__pyx_f_5pysam_10libchtslib__encodeFilename(PyObject *__pyx_v_filename) { | |
| ^ | |
| pysam/chtslib.c:1132:18: warning: ‘__pyx_f_5pysam_10libchtslib__forceStr’ defined but not used [-Wunused-function] | |
| static PyObject *__pyx_f_5pysam_10libchtslib__forceStr(PyObject *__pyx_v_s) { | |
| ^ | |
| pysam/chtslib.c:1473:18: warning: ‘__pyx_f_5pysam_10libchtslib__charptr_to_str’ defined but not used [-Wunused-function] | |
| static PyObject *__pyx_f_5pysam_10libchtslib__charptr_to_str(char *__pyx_v_s) { | |
| ^ | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-x86_64-2.7/pysam/htslib_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/kfunc.c -o build/temp.linux-x86_64-2.7/htslib/kfunc.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/vcfutils.c -o build/temp.linux-x86_64-2.7/htslib/vcfutils.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/sam.c -o build/temp.linux-x86_64-2.7/htslib/sam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/bgzf.c -o build/temp.linux-x86_64-2.7/htslib/bgzf.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/faidx.c -o build/temp.linux-x86_64-2.7/htslib/faidx.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/knetfile.c -o build/temp.linux-x86_64-2.7/htslib/knetfile.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/hfile_net.c -o build/temp.linux-x86_64-2.7/htslib/hfile_net.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/hts.c -o build/temp.linux-x86_64-2.7/htslib/hts.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/hfile.c -o build/temp.linux-x86_64-2.7/htslib/hfile.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/synced_bcf_reader.c -o build/temp.linux-x86_64-2.7/htslib/synced_bcf_reader.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/kstring.c -o build/temp.linux-x86_64-2.7/htslib/kstring.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/vcf_sweep.c -o build/temp.linux-x86_64-2.7/htslib/vcf_sweep.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/vcf.c -o build/temp.linux-x86_64-2.7/htslib/vcf.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/tbx.c -o build/temp.linux-x86_64-2.7/htslib/tbx.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/sam_header.c -o build/temp.linux-x86_64-2.7/htslib/cram/sam_header.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_encode.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_encode.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| htslib/cram/cram_encode.c: In function ‘process_one_read’: | |
| htslib/cram/cram_encode.c:2167:10: warning: unused variable ‘brg’ [-Wunused-variable] | |
| SAM_RG *brg = sam_hdr_find_rg(fd->header, "UNKNOWN"); | |
| ^ | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/string_alloc.c -o build/temp.linux-x86_64-2.7/htslib/cram/string_alloc.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/thread_pool.c -o build/temp.linux-x86_64-2.7/htslib/cram/thread_pool.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_index.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_index.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| htslib/cram/cram_index.c: In function ‘cram_index_build’: | |
| htslib/cram/cram_index.c:431:23: warning: variable ‘hpos’ set but not used [-Wunused-but-set-variable] | |
| off_t cpos, spos, hpos; | |
| ^ | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/mFILE.c -o build/temp.linux-x86_64-2.7/htslib/cram/mFILE.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_samtools.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_samtools.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/pooled_alloc.c -o build/temp.linux-x86_64-2.7/htslib/cram/pooled_alloc.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/open_trace_file.c -o build/temp.linux-x86_64-2.7/htslib/cram/open_trace_file.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/zfio.c -o build/temp.linux-x86_64-2.7/htslib/cram/zfio.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/files.c -o build/temp.linux-x86_64-2.7/htslib/cram/files.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_decode.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_decode.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_codecs.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_codecs.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/md5.c -o build/temp.linux-x86_64-2.7/htslib/cram/md5.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_io.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_io.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/vlen.c -o build/temp.linux-x86_64-2.7/htslib/cram/vlen.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| htslib/cram/vlen.c: In function ‘vflen’: | |
| htslib/cram/vlen.c:121:9: warning: variable ‘i’ set but not used [-Wunused-but-set-variable] | |
| int i; | |
| ^ | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_stats.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_stats.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/pysam/chtslib.o build/temp.linux-x86_64-2.7/pysam/htslib_util.o build/temp.linux-x86_64-2.7/htslib/kfunc.o build/temp.linux-x86_64-2.7/htslib/vcfutils.o build/temp.linux-x86_64-2.7/htslib/sam.o build/temp.linux-x86_64-2.7/htslib/bgzf.o build/temp.linux-x86_64-2.7/htslib/faidx.o build/temp.linux-x86_64-2.7/htslib/knetfile.o build/temp.linux-x86_64-2.7/htslib/hfile_net.o build/temp.linux-x86_64-2.7/htslib/hts.o build/temp.linux-x86_64-2.7/htslib/hfile.o build/temp.linux-x86_64-2.7/htslib/synced_bcf_reader.o build/temp.linux-x86_64-2.7/htslib/kstring.o build/temp.linux-x86_64-2.7/htslib/vcf_sweep.o build/temp.linux-x86_64-2.7/htslib/vcf.o build/temp.linux-x86_64-2.7/htslib/tbx.o build/temp.linux-x86_64-2.7/htslib/cram/sam_header.o build/temp.linux-x86_64-2.7/htslib/cram/cram_encode.o build/temp.linux-x86_64-2.7/htslib/cram/string_alloc.o build/temp.linux-x86_64-2.7/htslib/cram/thread_pool.o build/temp.linux-x86_64-2.7/htslib/cram/cram_index.o build/temp.linux-x86_64-2.7/htslib/cram/mFILE.o build/temp.linux-x86_64-2.7/htslib/cram/cram_samtools.o build/temp.linux-x86_64-2.7/htslib/cram/pooled_alloc.o build/temp.linux-x86_64-2.7/htslib/cram/open_trace_file.o build/temp.linux-x86_64-2.7/htslib/cram/zfio.o build/temp.linux-x86_64-2.7/htslib/cram/files.o build/temp.linux-x86_64-2.7/htslib/cram/cram_decode.o build/temp.linux-x86_64-2.7/htslib/cram/cram_codecs.o build/temp.linux-x86_64-2.7/htslib/cram/md5.o build/temp.linux-x86_64-2.7/htslib/cram/cram_io.o build/temp.linux-x86_64-2.7/htslib/cram/vlen.o build/temp.linux-x86_64-2.7/htslib/cram/cram_stats.o -lz -o build/lib.linux-x86_64-2.7/pysam/libchtslib.so | |
| building 'pysam.csamfile' extension | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c pysam/csamfile.c -o build/temp.linux-x86_64-2.7/pysam/csamfile.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| In file included from pysam/pysam_stream.h:4:0, | |
| from pysam/csamfile.c:353: | |
| htslib/htslib/kseq.h:170:16: warning: ‘kseq_init’ defined but not used [-Wunused-function] | |
| SCOPE kseq_t *kseq_init(type_t fd) \ | |
| ^ | |
| htslib/htslib/kseq.h:241:2: note: in expansion of macro ‘__KSEQ_BASIC’ | |
| __KSEQ_BASIC(SCOPE, type_t) \ | |
| ^ | |
| htslib/htslib/kseq.h:244:35: note: in expansion of macro ‘KSEQ_INIT2’ | |
| #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | |
| ^ | |
| pysam/pysam_stream.h:8:1: note: in expansion of macro ‘KSEQ_INIT’ | |
| KSEQ_INIT(gzFile, gzread) | |
| ^ | |
| htslib/htslib/kseq.h:176:13: warning: ‘kseq_destroy’ defined but not used [-Wunused-function] | |
| SCOPE void kseq_destroy(kseq_t *ks) \ | |
| ^ | |
| htslib/htslib/kseq.h:241:2: note: in expansion of macro ‘__KSEQ_BASIC’ | |
| __KSEQ_BASIC(SCOPE, type_t) \ | |
| ^ | |
| htslib/htslib/kseq.h:244:35: note: in expansion of macro ‘KSEQ_INIT2’ | |
| #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | |
| ^ | |
| pysam/pysam_stream.h:8:1: note: in expansion of macro ‘KSEQ_INIT’ | |
| KSEQ_INIT(gzFile, gzread) | |
| ^ | |
| htslib/htslib/kseq.h:190:12: warning: ‘kseq_read’ defined but not used [-Wunused-function] | |
| SCOPE int kseq_read(kseq_t *seq) \ | |
| ^ | |
| htslib/htslib/kseq.h:242:2: note: in expansion of macro ‘__KSEQ_READ’ | |
| __KSEQ_READ(SCOPE) | |
| ^ | |
| htslib/htslib/kseq.h:244:35: note: in expansion of macro ‘KSEQ_INIT2’ | |
| #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | |
| ^ | |
| pysam/pysam_stream.h:8:1: note: in expansion of macro ‘KSEQ_INIT’ | |
| KSEQ_INIT(gzFile, gzread) | |
| ^ | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-x86_64-2.7/pysam/htslib_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c pysam/samfile_util.c -o build/temp.linux-x86_64-2.7/pysam/samfile_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c samtools/kprobaln.c -o build/temp.linux-x86_64-2.7/samtools/kprobaln.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| samtools/kprobaln.c: In function ‘kpa_glocal’: | |
| samtools/kprobaln.c:78:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable] | |
| int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr; | |
| ^ | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/kfunc.c -o build/temp.linux-x86_64-2.7/htslib/kfunc.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/vcfutils.c -o build/temp.linux-x86_64-2.7/htslib/vcfutils.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/sam.c -o build/temp.linux-x86_64-2.7/htslib/sam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/bgzf.c -o build/temp.linux-x86_64-2.7/htslib/bgzf.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/faidx.c -o build/temp.linux-x86_64-2.7/htslib/faidx.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/knetfile.c -o build/temp.linux-x86_64-2.7/htslib/knetfile.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/hfile_net.c -o build/temp.linux-x86_64-2.7/htslib/hfile_net.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/hts.c -o build/temp.linux-x86_64-2.7/htslib/hts.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/hfile.c -o build/temp.linux-x86_64-2.7/htslib/hfile.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/synced_bcf_reader.c -o build/temp.linux-x86_64-2.7/htslib/synced_bcf_reader.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/kstring.c -o build/temp.linux-x86_64-2.7/htslib/kstring.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/vcf_sweep.c -o build/temp.linux-x86_64-2.7/htslib/vcf_sweep.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/vcf.c -o build/temp.linux-x86_64-2.7/htslib/vcf.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/tbx.c -o build/temp.linux-x86_64-2.7/htslib/tbx.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/sam_header.c -o build/temp.linux-x86_64-2.7/htslib/cram/sam_header.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_encode.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_encode.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| htslib/cram/cram_encode.c: In function ‘process_one_read’: | |
| htslib/cram/cram_encode.c:2167:10: warning: unused variable ‘brg’ [-Wunused-variable] | |
| SAM_RG *brg = sam_hdr_find_rg(fd->header, "UNKNOWN"); | |
| ^ | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/string_alloc.c -o build/temp.linux-x86_64-2.7/htslib/cram/string_alloc.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/thread_pool.c -o build/temp.linux-x86_64-2.7/htslib/cram/thread_pool.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_index.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_index.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| htslib/cram/cram_index.c: In function ‘cram_index_build’: | |
| htslib/cram/cram_index.c:431:23: warning: variable ‘hpos’ set but not used [-Wunused-but-set-variable] | |
| off_t cpos, spos, hpos; | |
| ^ | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/mFILE.c -o build/temp.linux-x86_64-2.7/htslib/cram/mFILE.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_samtools.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_samtools.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/pooled_alloc.c -o build/temp.linux-x86_64-2.7/htslib/cram/pooled_alloc.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/open_trace_file.c -o build/temp.linux-x86_64-2.7/htslib/cram/open_trace_file.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/zfio.c -o build/temp.linux-x86_64-2.7/htslib/cram/zfio.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/files.c -o build/temp.linux-x86_64-2.7/htslib/cram/files.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_decode.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_decode.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_codecs.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_codecs.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/md5.c -o build/temp.linux-x86_64-2.7/htslib/cram/md5.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_io.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_io.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/vlen.c -o build/temp.linux-x86_64-2.7/htslib/cram/vlen.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| htslib/cram/vlen.c: In function ‘vflen’: | |
| htslib/cram/vlen.c:121:9: warning: variable ‘i’ set but not used [-Wunused-but-set-variable] | |
| int i; | |
| ^ | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_stats.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_stats.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/pysam/csamfile.o build/temp.linux-x86_64-2.7/pysam/htslib_util.o build/temp.linux-x86_64-2.7/pysam/samfile_util.o build/temp.linux-x86_64-2.7/samtools/kprobaln.o build/temp.linux-x86_64-2.7/htslib/kfunc.o build/temp.linux-x86_64-2.7/htslib/vcfutils.o build/temp.linux-x86_64-2.7/htslib/sam.o build/temp.linux-x86_64-2.7/htslib/bgzf.o build/temp.linux-x86_64-2.7/htslib/faidx.o build/temp.linux-x86_64-2.7/htslib/knetfile.o build/temp.linux-x86_64-2.7/htslib/hfile_net.o build/temp.linux-x86_64-2.7/htslib/hts.o build/temp.linux-x86_64-2.7/htslib/hfile.o build/temp.linux-x86_64-2.7/htslib/synced_bcf_reader.o build/temp.linux-x86_64-2.7/htslib/kstring.o build/temp.linux-x86_64-2.7/htslib/vcf_sweep.o build/temp.linux-x86_64-2.7/htslib/vcf.o build/temp.linux-x86_64-2.7/htslib/tbx.o build/temp.linux-x86_64-2.7/htslib/cram/sam_header.o build/temp.linux-x86_64-2.7/htslib/cram/cram_encode.o build/temp.linux-x86_64-2.7/htslib/cram/string_alloc.o build/temp.linux-x86_64-2.7/htslib/cram/thread_pool.o build/temp.linux-x86_64-2.7/htslib/cram/cram_index.o build/temp.linux-x86_64-2.7/htslib/cram/mFILE.o build/temp.linux-x86_64-2.7/htslib/cram/cram_samtools.o build/temp.linux-x86_64-2.7/htslib/cram/pooled_alloc.o build/temp.linux-x86_64-2.7/htslib/cram/open_trace_file.o build/temp.linux-x86_64-2.7/htslib/cram/zfio.o build/temp.linux-x86_64-2.7/htslib/cram/files.o build/temp.linux-x86_64-2.7/htslib/cram/cram_decode.o build/temp.linux-x86_64-2.7/htslib/cram/cram_codecs.o build/temp.linux-x86_64-2.7/htslib/cram/md5.o build/temp.linux-x86_64-2.7/htslib/cram/cram_io.o build/temp.linux-x86_64-2.7/htslib/cram/vlen.o build/temp.linux-x86_64-2.7/htslib/cram/cram_stats.o -lz -o build/lib.linux-x86_64-2.7/pysam/csamfile.so | |
| building 'pysam.calignmentfile' extension | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c pysam/calignmentfile.c -o build/temp.linux-x86_64-2.7/pysam/calignmentfile.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| pysam/calignmentfile.c: In function ‘__pyx_f_5pysam_14calignmentfile_14IteratorColumn_cnext’: | |
| pysam/calignmentfile.c:19348:21: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default] | |
| __pyx_v_self->plp = bam_plp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp)); | |
| ^ | |
| In file included from pysam/pysam_stream.h:4:0, | |
| from pysam/calignmentfile.c:353: | |
| pysam/calignmentfile.c: At top level: | |
| htslib/htslib/kseq.h:170:16: warning: ‘kseq_init’ defined but not used [-Wunused-function] | |
| SCOPE kseq_t *kseq_init(type_t fd) \ | |
| ^ | |
| htslib/htslib/kseq.h:241:2: note: in expansion of macro ‘__KSEQ_BASIC’ | |
| __KSEQ_BASIC(SCOPE, type_t) \ | |
| ^ | |
| htslib/htslib/kseq.h:244:35: note: in expansion of macro ‘KSEQ_INIT2’ | |
| #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | |
| ^ | |
| pysam/pysam_stream.h:8:1: note: in expansion of macro ‘KSEQ_INIT’ | |
| KSEQ_INIT(gzFile, gzread) | |
| ^ | |
| htslib/htslib/kseq.h:176:13: warning: ‘kseq_destroy’ defined but not used [-Wunused-function] | |
| SCOPE void kseq_destroy(kseq_t *ks) \ | |
| ^ | |
| htslib/htslib/kseq.h:241:2: note: in expansion of macro ‘__KSEQ_BASIC’ | |
| __KSEQ_BASIC(SCOPE, type_t) \ | |
| ^ | |
| htslib/htslib/kseq.h:244:35: note: in expansion of macro ‘KSEQ_INIT2’ | |
| #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | |
| ^ | |
| pysam/pysam_stream.h:8:1: note: in expansion of macro ‘KSEQ_INIT’ | |
| KSEQ_INIT(gzFile, gzread) | |
| ^ | |
| htslib/htslib/kseq.h:190:12: warning: ‘kseq_read’ defined but not used [-Wunused-function] | |
| SCOPE int kseq_read(kseq_t *seq) \ | |
| ^ | |
| htslib/htslib/kseq.h:242:2: note: in expansion of macro ‘__KSEQ_READ’ | |
| __KSEQ_READ(SCOPE) | |
| ^ | |
| htslib/htslib/kseq.h:244:35: note: in expansion of macro ‘KSEQ_INIT2’ | |
| #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | |
| ^ | |
| pysam/pysam_stream.h:8:1: note: in expansion of macro ‘KSEQ_INIT’ | |
| KSEQ_INIT(gzFile, gzread) | |
| ^ | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-x86_64-2.7/pysam/htslib_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c pysam/samfile_util.c -o build/temp.linux-x86_64-2.7/pysam/samfile_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c samtools/kprobaln.c -o build/temp.linux-x86_64-2.7/samtools/kprobaln.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| samtools/kprobaln.c: In function ‘kpa_glocal’: | |
| samtools/kprobaln.c:78:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable] | |
| int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr; | |
| ^ | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/kfunc.c -o build/temp.linux-x86_64-2.7/htslib/kfunc.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/vcfutils.c -o build/temp.linux-x86_64-2.7/htslib/vcfutils.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/sam.c -o build/temp.linux-x86_64-2.7/htslib/sam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/bgzf.c -o build/temp.linux-x86_64-2.7/htslib/bgzf.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/faidx.c -o build/temp.linux-x86_64-2.7/htslib/faidx.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/knetfile.c -o build/temp.linux-x86_64-2.7/htslib/knetfile.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/hfile_net.c -o build/temp.linux-x86_64-2.7/htslib/hfile_net.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/hts.c -o build/temp.linux-x86_64-2.7/htslib/hts.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/hfile.c -o build/temp.linux-x86_64-2.7/htslib/hfile.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/synced_bcf_reader.c -o build/temp.linux-x86_64-2.7/htslib/synced_bcf_reader.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/kstring.c -o build/temp.linux-x86_64-2.7/htslib/kstring.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/vcf_sweep.c -o build/temp.linux-x86_64-2.7/htslib/vcf_sweep.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/vcf.c -o build/temp.linux-x86_64-2.7/htslib/vcf.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/tbx.c -o build/temp.linux-x86_64-2.7/htslib/tbx.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/sam_header.c -o build/temp.linux-x86_64-2.7/htslib/cram/sam_header.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_encode.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_encode.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| htslib/cram/cram_encode.c: In function ‘process_one_read’: | |
| htslib/cram/cram_encode.c:2167:10: warning: unused variable ‘brg’ [-Wunused-variable] | |
| SAM_RG *brg = sam_hdr_find_rg(fd->header, "UNKNOWN"); | |
| ^ | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/string_alloc.c -o build/temp.linux-x86_64-2.7/htslib/cram/string_alloc.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/thread_pool.c -o build/temp.linux-x86_64-2.7/htslib/cram/thread_pool.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_index.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_index.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| htslib/cram/cram_index.c: In function ‘cram_index_build’: | |
| htslib/cram/cram_index.c:431:23: warning: variable ‘hpos’ set but not used [-Wunused-but-set-variable] | |
| off_t cpos, spos, hpos; | |
| ^ | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/mFILE.c -o build/temp.linux-x86_64-2.7/htslib/cram/mFILE.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_samtools.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_samtools.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/pooled_alloc.c -o build/temp.linux-x86_64-2.7/htslib/cram/pooled_alloc.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/open_trace_file.c -o build/temp.linux-x86_64-2.7/htslib/cram/open_trace_file.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/zfio.c -o build/temp.linux-x86_64-2.7/htslib/cram/zfio.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/files.c -o build/temp.linux-x86_64-2.7/htslib/cram/files.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_decode.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_decode.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_codecs.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_codecs.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/md5.c -o build/temp.linux-x86_64-2.7/htslib/cram/md5.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_io.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_io.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/vlen.c -o build/temp.linux-x86_64-2.7/htslib/cram/vlen.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| htslib/cram/vlen.c: In function ‘vflen’: | |
| htslib/cram/vlen.c:121:9: warning: variable ‘i’ set but not used [-Wunused-but-set-variable] | |
| int i; | |
| ^ | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Isamtools -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_stats.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_stats.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/pysam/calignmentfile.o build/temp.linux-x86_64-2.7/pysam/htslib_util.o build/temp.linux-x86_64-2.7/pysam/samfile_util.o build/temp.linux-x86_64-2.7/samtools/kprobaln.o build/temp.linux-x86_64-2.7/htslib/kfunc.o build/temp.linux-x86_64-2.7/htslib/vcfutils.o build/temp.linux-x86_64-2.7/htslib/sam.o build/temp.linux-x86_64-2.7/htslib/bgzf.o build/temp.linux-x86_64-2.7/htslib/faidx.o build/temp.linux-x86_64-2.7/htslib/knetfile.o build/temp.linux-x86_64-2.7/htslib/hfile_net.o build/temp.linux-x86_64-2.7/htslib/hts.o build/temp.linux-x86_64-2.7/htslib/hfile.o build/temp.linux-x86_64-2.7/htslib/synced_bcf_reader.o build/temp.linux-x86_64-2.7/htslib/kstring.o build/temp.linux-x86_64-2.7/htslib/vcf_sweep.o build/temp.linux-x86_64-2.7/htslib/vcf.o build/temp.linux-x86_64-2.7/htslib/tbx.o build/temp.linux-x86_64-2.7/htslib/cram/sam_header.o build/temp.linux-x86_64-2.7/htslib/cram/cram_encode.o build/temp.linux-x86_64-2.7/htslib/cram/string_alloc.o build/temp.linux-x86_64-2.7/htslib/cram/thread_pool.o build/temp.linux-x86_64-2.7/htslib/cram/cram_index.o build/temp.linux-x86_64-2.7/htslib/cram/mFILE.o build/temp.linux-x86_64-2.7/htslib/cram/cram_samtools.o build/temp.linux-x86_64-2.7/htslib/cram/pooled_alloc.o build/temp.linux-x86_64-2.7/htslib/cram/open_trace_file.o build/temp.linux-x86_64-2.7/htslib/cram/zfio.o build/temp.linux-x86_64-2.7/htslib/cram/files.o build/temp.linux-x86_64-2.7/htslib/cram/cram_decode.o build/temp.linux-x86_64-2.7/htslib/cram/cram_codecs.o build/temp.linux-x86_64-2.7/htslib/cram/md5.o build/temp.linux-x86_64-2.7/htslib/cram/cram_io.o build/temp.linux-x86_64-2.7/htslib/cram/vlen.o build/temp.linux-x86_64-2.7/htslib/cram/cram_stats.o -lz -o build/lib.linux-x86_64-2.7/pysam/calignmentfile.so | |
| building 'pysam.ctabix' extension | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c pysam/ctabix.c -o build/temp.linux-x86_64-2.7/pysam/ctabix.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| pysam/ctabix.c: In function ‘__pyx_pf_5pysam_6ctabix_9TabixFile_7contigs___get__’: | |
| pysam/ctabix.c:5116:21: warning: assignment from incompatible pointer type [enabled by default] | |
| __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences)); | |
| ^ | |
| pysam/ctabix.c: In function ‘__pyx_f_5pysam_6ctabix_buildGzipError’: | |
| pysam/ctabix.c:8982:13: warning: assignment discards ‘const’ qualifier from pointer target type [enabled by default] | |
| __pyx_v_s = gzerror(__pyx_v_gzfp, (&__pyx_v_errnum)); | |
| ^ | |
| In file included from pysam/pysam_stream.h:4:0, | |
| from pysam/ctabix.c:355: | |
| pysam/ctabix.c: At top level: | |
| htslib/htslib/kseq.h:170:16: warning: ‘kseq_init’ defined but not used [-Wunused-function] | |
| SCOPE kseq_t *kseq_init(type_t fd) \ | |
| ^ | |
| htslib/htslib/kseq.h:241:2: note: in expansion of macro ‘__KSEQ_BASIC’ | |
| __KSEQ_BASIC(SCOPE, type_t) \ | |
| ^ | |
| htslib/htslib/kseq.h:244:35: note: in expansion of macro ‘KSEQ_INIT2’ | |
| #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | |
| ^ | |
| pysam/pysam_stream.h:8:1: note: in expansion of macro ‘KSEQ_INIT’ | |
| KSEQ_INIT(gzFile, gzread) | |
| ^ | |
| htslib/htslib/kseq.h:176:13: warning: ‘kseq_destroy’ defined but not used [-Wunused-function] | |
| SCOPE void kseq_destroy(kseq_t *ks) \ | |
| ^ | |
| htslib/htslib/kseq.h:241:2: note: in expansion of macro ‘__KSEQ_BASIC’ | |
| __KSEQ_BASIC(SCOPE, type_t) \ | |
| ^ | |
| htslib/htslib/kseq.h:244:35: note: in expansion of macro ‘KSEQ_INIT2’ | |
| #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | |
| ^ | |
| pysam/pysam_stream.h:8:1: note: in expansion of macro ‘KSEQ_INIT’ | |
| KSEQ_INIT(gzFile, gzread) | |
| ^ | |
| htslib/htslib/kseq.h:190:12: warning: ‘kseq_read’ defined but not used [-Wunused-function] | |
| SCOPE int kseq_read(kseq_t *seq) \ | |
| ^ | |
| htslib/htslib/kseq.h:242:2: note: in expansion of macro ‘__KSEQ_READ’ | |
| __KSEQ_READ(SCOPE) | |
| ^ | |
| htslib/htslib/kseq.h:244:35: note: in expansion of macro ‘KSEQ_INIT2’ | |
| #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | |
| ^ | |
| pysam/pysam_stream.h:8:1: note: in expansion of macro ‘KSEQ_INIT’ | |
| KSEQ_INIT(gzFile, gzread) | |
| ^ | |
| pysam/ctabix.c:8951:18: warning: ‘__pyx_f_5pysam_6ctabix_buildGzipError’ defined but not used [-Wunused-function] | |
| static PyObject *__pyx_f_5pysam_6ctabix_buildGzipError(void *__pyx_v_gzfp) { | |
| ^ | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c pysam/tabix_util.c -o build/temp.linux-x86_64-2.7/pysam/tabix_util.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/kfunc.c -o build/temp.linux-x86_64-2.7/htslib/kfunc.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/vcfutils.c -o build/temp.linux-x86_64-2.7/htslib/vcfutils.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/sam.c -o build/temp.linux-x86_64-2.7/htslib/sam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/bgzf.c -o build/temp.linux-x86_64-2.7/htslib/bgzf.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/faidx.c -o build/temp.linux-x86_64-2.7/htslib/faidx.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/knetfile.c -o build/temp.linux-x86_64-2.7/htslib/knetfile.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/hfile_net.c -o build/temp.linux-x86_64-2.7/htslib/hfile_net.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/hts.c -o build/temp.linux-x86_64-2.7/htslib/hts.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/hfile.c -o build/temp.linux-x86_64-2.7/htslib/hfile.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/synced_bcf_reader.c -o build/temp.linux-x86_64-2.7/htslib/synced_bcf_reader.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/kstring.c -o build/temp.linux-x86_64-2.7/htslib/kstring.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/vcf_sweep.c -o build/temp.linux-x86_64-2.7/htslib/vcf_sweep.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/vcf.c -o build/temp.linux-x86_64-2.7/htslib/vcf.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/tbx.c -o build/temp.linux-x86_64-2.7/htslib/tbx.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/sam_header.c -o build/temp.linux-x86_64-2.7/htslib/cram/sam_header.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_encode.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_encode.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| htslib/cram/cram_encode.c: In function ‘process_one_read’: | |
| htslib/cram/cram_encode.c:2167:10: warning: unused variable ‘brg’ [-Wunused-variable] | |
| SAM_RG *brg = sam_hdr_find_rg(fd->header, "UNKNOWN"); | |
| ^ | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/string_alloc.c -o build/temp.linux-x86_64-2.7/htslib/cram/string_alloc.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/thread_pool.c -o build/temp.linux-x86_64-2.7/htslib/cram/thread_pool.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_index.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_index.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| htslib/cram/cram_index.c: In function ‘cram_index_build’: | |
| htslib/cram/cram_index.c:431:23: warning: variable ‘hpos’ set but not used [-Wunused-but-set-variable] | |
| off_t cpos, spos, hpos; | |
| ^ | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/mFILE.c -o build/temp.linux-x86_64-2.7/htslib/cram/mFILE.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_samtools.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_samtools.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/pooled_alloc.c -o build/temp.linux-x86_64-2.7/htslib/cram/pooled_alloc.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/open_trace_file.c -o build/temp.linux-x86_64-2.7/htslib/cram/open_trace_file.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/zfio.c -o build/temp.linux-x86_64-2.7/htslib/cram/zfio.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/files.c -o build/temp.linux-x86_64-2.7/htslib/cram/files.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_decode.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_decode.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_codecs.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_codecs.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/md5.c -o build/temp.linux-x86_64-2.7/htslib/cram/md5.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_io.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_io.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/vlen.c -o build/temp.linux-x86_64-2.7/htslib/cram/vlen.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| htslib/cram/vlen.c: In function ‘vflen’: | |
| htslib/cram/vlen.c:121:9: warning: variable ‘i’ set but not used [-Wunused-but-set-variable] | |
| int i; | |
| ^ | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_stats.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_stats.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/pysam/ctabix.o build/temp.linux-x86_64-2.7/pysam/tabix_util.o build/temp.linux-x86_64-2.7/htslib/kfunc.o build/temp.linux-x86_64-2.7/htslib/vcfutils.o build/temp.linux-x86_64-2.7/htslib/sam.o build/temp.linux-x86_64-2.7/htslib/bgzf.o build/temp.linux-x86_64-2.7/htslib/faidx.o build/temp.linux-x86_64-2.7/htslib/knetfile.o build/temp.linux-x86_64-2.7/htslib/hfile_net.o build/temp.linux-x86_64-2.7/htslib/hts.o build/temp.linux-x86_64-2.7/htslib/hfile.o build/temp.linux-x86_64-2.7/htslib/synced_bcf_reader.o build/temp.linux-x86_64-2.7/htslib/kstring.o build/temp.linux-x86_64-2.7/htslib/vcf_sweep.o build/temp.linux-x86_64-2.7/htslib/vcf.o build/temp.linux-x86_64-2.7/htslib/tbx.o build/temp.linux-x86_64-2.7/htslib/cram/sam_header.o build/temp.linux-x86_64-2.7/htslib/cram/cram_encode.o build/temp.linux-x86_64-2.7/htslib/cram/string_alloc.o build/temp.linux-x86_64-2.7/htslib/cram/thread_pool.o build/temp.linux-x86_64-2.7/htslib/cram/cram_index.o build/temp.linux-x86_64-2.7/htslib/cram/mFILE.o build/temp.linux-x86_64-2.7/htslib/cram/cram_samtools.o build/temp.linux-x86_64-2.7/htslib/cram/pooled_alloc.o build/temp.linux-x86_64-2.7/htslib/cram/open_trace_file.o build/temp.linux-x86_64-2.7/htslib/cram/zfio.o build/temp.linux-x86_64-2.7/htslib/cram/files.o build/temp.linux-x86_64-2.7/htslib/cram/cram_decode.o build/temp.linux-x86_64-2.7/htslib/cram/cram_codecs.o build/temp.linux-x86_64-2.7/htslib/cram/md5.o build/temp.linux-x86_64-2.7/htslib/cram/cram_io.o build/temp.linux-x86_64-2.7/htslib/cram/vlen.o build/temp.linux-x86_64-2.7/htslib/cram/cram_stats.o -Lpysam -lz -o build/lib.linux-x86_64-2.7/pysam/ctabix.so | |
| building 'pysam.TabProxies' extension | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/include/python2.7 -c pysam/TabProxies.c -o build/temp.linux-x86_64-2.7/pysam/TabProxies.o -Wno-error=declaration-after-statement | |
| pysam/TabProxies.c:1464:18: warning: ‘__pyx_f_5pysam_10TabProxies_from_string_and_size’ defined but not used [-Wunused-function] | |
| static PyObject *__pyx_f_5pysam_10TabProxies_from_string_and_size(char *__pyx_v_s, size_t __pyx_v_length) { | |
| ^ | |
| pysam/TabProxies.c:1759:18: warning: ‘__pyx_f_5pysam_10TabProxies__charptr_to_str’ defined but not used [-Wunused-function] | |
| static PyObject *__pyx_f_5pysam_10TabProxies__charptr_to_str(char *__pyx_v_s, struct __pyx_opt_args_5pysam_10TabProxies__charptr_to_str *__pyx_optional_args) { | |
| ^ | |
| pysam/TabProxies.c:2002:14: warning: ‘__pyx_f_5pysam_10TabProxies_nextItem’ defined but not used [-Wunused-function] | |
| static char *__pyx_f_5pysam_10TabProxies_nextItem(char *__pyx_v_buffer) { | |
| ^ | |
| x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/pysam/TabProxies.o -lz -o build/lib.linux-x86_64-2.7/pysam/TabProxies.so | |
| building 'pysam.cvcf' extension | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -Ihtslib -Ihtslib -I/usr/include/python2.7 -c pysam/cvcf.c -o build/temp.linux-x86_64-2.7/pysam/cvcf.o -Wno-error=declaration-after-statement | |
| In file included from pysam/pysam_stream.h:4:0, | |
| from pysam/cvcf.c:355: | |
| htslib/htslib/kseq.h:170:16: warning: ‘kseq_init’ defined but not used [-Wunused-function] | |
| SCOPE kseq_t *kseq_init(type_t fd) \ | |
| ^ | |
| htslib/htslib/kseq.h:241:2: note: in expansion of macro ‘__KSEQ_BASIC’ | |
| __KSEQ_BASIC(SCOPE, type_t) \ | |
| ^ | |
| htslib/htslib/kseq.h:244:35: note: in expansion of macro ‘KSEQ_INIT2’ | |
| #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | |
| ^ | |
| pysam/pysam_stream.h:8:1: note: in expansion of macro ‘KSEQ_INIT’ | |
| KSEQ_INIT(gzFile, gzread) | |
| ^ | |
| htslib/htslib/kseq.h:176:13: warning: ‘kseq_destroy’ defined but not used [-Wunused-function] | |
| SCOPE void kseq_destroy(kseq_t *ks) \ | |
| ^ | |
| htslib/htslib/kseq.h:241:2: note: in expansion of macro ‘__KSEQ_BASIC’ | |
| __KSEQ_BASIC(SCOPE, type_t) \ | |
| ^ | |
| htslib/htslib/kseq.h:244:35: note: in expansion of macro ‘KSEQ_INIT2’ | |
| #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | |
| ^ | |
| pysam/pysam_stream.h:8:1: note: in expansion of macro ‘KSEQ_INIT’ | |
| KSEQ_INIT(gzFile, gzread) | |
| ^ | |
| htslib/htslib/kseq.h:190:12: warning: ‘kseq_read’ defined but not used [-Wunused-function] | |
| SCOPE int kseq_read(kseq_t *seq) \ | |
| ^ | |
| htslib/htslib/kseq.h:242:2: note: in expansion of macro ‘__KSEQ_READ’ | |
| __KSEQ_READ(SCOPE) | |
| ^ | |
| htslib/htslib/kseq.h:244:35: note: in expansion of macro ‘KSEQ_INIT2’ | |
| #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | |
| ^ | |
| pysam/pysam_stream.h:8:1: note: in expansion of macro ‘KSEQ_INIT’ | |
| KSEQ_INIT(gzFile, gzread) | |
| ^ | |
| pysam/cvcf.c: In function ‘__pyx_pw_5pysam_4cvcf_3VCF_33parse_data’: | |
| pysam/cvcf.c:18544:33: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized] | |
| __pyx_t_2 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 858; __pyx_clineno = __LINE__; goto __pyx_L1_error;} | |
| ^ | |
| pysam/cvcf.c:14888:10: note: ‘__pyx_v_qual’ was declared here | |
| double __pyx_v_qual; | |
| ^ | |
| x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/pysam/cvcf.o -lz -o build/lib.linux-x86_64-2.7/pysam/cvcf.so | |
| building 'pysam.cfaidx' extension | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c pysam/cfaidx.c -o build/temp.linux-x86_64-2.7/pysam/cfaidx.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/kfunc.c -o build/temp.linux-x86_64-2.7/htslib/kfunc.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/vcfutils.c -o build/temp.linux-x86_64-2.7/htslib/vcfutils.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/sam.c -o build/temp.linux-x86_64-2.7/htslib/sam.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/bgzf.c -o build/temp.linux-x86_64-2.7/htslib/bgzf.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/faidx.c -o build/temp.linux-x86_64-2.7/htslib/faidx.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/knetfile.c -o build/temp.linux-x86_64-2.7/htslib/knetfile.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/hfile_net.c -o build/temp.linux-x86_64-2.7/htslib/hfile_net.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/hts.c -o build/temp.linux-x86_64-2.7/htslib/hts.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/hfile.c -o build/temp.linux-x86_64-2.7/htslib/hfile.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/synced_bcf_reader.c -o build/temp.linux-x86_64-2.7/htslib/synced_bcf_reader.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/kstring.c -o build/temp.linux-x86_64-2.7/htslib/kstring.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/vcf_sweep.c -o build/temp.linux-x86_64-2.7/htslib/vcf_sweep.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/vcf.c -o build/temp.linux-x86_64-2.7/htslib/vcf.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/tbx.c -o build/temp.linux-x86_64-2.7/htslib/tbx.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/sam_header.c -o build/temp.linux-x86_64-2.7/htslib/cram/sam_header.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_encode.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_encode.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| htslib/cram/cram_encode.c: In function ‘process_one_read’: | |
| htslib/cram/cram_encode.c:2167:10: warning: unused variable ‘brg’ [-Wunused-variable] | |
| SAM_RG *brg = sam_hdr_find_rg(fd->header, "UNKNOWN"); | |
| ^ | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/string_alloc.c -o build/temp.linux-x86_64-2.7/htslib/cram/string_alloc.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/thread_pool.c -o build/temp.linux-x86_64-2.7/htslib/cram/thread_pool.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_index.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_index.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| htslib/cram/cram_index.c: In function ‘cram_index_build’: | |
| htslib/cram/cram_index.c:431:23: warning: variable ‘hpos’ set but not used [-Wunused-but-set-variable] | |
| off_t cpos, spos, hpos; | |
| ^ | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/mFILE.c -o build/temp.linux-x86_64-2.7/htslib/cram/mFILE.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_samtools.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_samtools.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/pooled_alloc.c -o build/temp.linux-x86_64-2.7/htslib/cram/pooled_alloc.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/open_trace_file.c -o build/temp.linux-x86_64-2.7/htslib/cram/open_trace_file.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/zfio.c -o build/temp.linux-x86_64-2.7/htslib/cram/zfio.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/files.c -o build/temp.linux-x86_64-2.7/htslib/cram/files.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_decode.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_decode.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_codecs.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_codecs.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/md5.c -o build/temp.linux-x86_64-2.7/htslib/cram/md5.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_io.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_io.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/vlen.c -o build/temp.linux-x86_64-2.7/htslib/cram/vlen.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| htslib/cram/vlen.c: In function ‘vflen’: | |
| htslib/cram/vlen.c:121:9: warning: variable ‘i’ set but not used [-Wunused-but-set-variable] | |
| int i; | |
| ^ | |
| x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Ipysam -Ihtslib -I/usr/include/python2.7 -c htslib/cram/cram_stats.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_stats.o -Wno-error=declaration-after-statement -DSAMTOOLS=1 | |
| x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/pysam/cfaidx.o build/temp.linux-x86_64-2.7/htslib/kfunc.o build/temp.linux-x86_64-2.7/htslib/vcfutils.o build/temp.linux-x86_64-2.7/htslib/sam.o build/temp.linux-x86_64-2.7/htslib/bgzf.o build/temp.linux-x86_64-2.7/htslib/faidx.o build/temp.linux-x86_64-2.7/htslib/knetfile.o build/temp.linux-x86_64-2.7/htslib/hfile_net.o build/temp.linux-x86_64-2.7/htslib/hts.o build/temp.linux-x86_64-2.7/htslib/hfile.o build/temp.linux-x86_64-2.7/htslib/synced_bcf_reader.o build/temp.linux-x86_64-2.7/htslib/kstring.o build/temp.linux-x86_64-2.7/htslib/vcf_sweep.o build/temp.linux-x86_64-2.7/htslib/vcf.o build/temp.linux-x86_64-2.7/htslib/tbx.o build/temp.linux-x86_64-2.7/htslib/cram/sam_header.o build/temp.linux-x86_64-2.7/htslib/cram/cram_encode.o build/temp.linux-x86_64-2.7/htslib/cram/string_alloc.o build/temp.linux-x86_64-2.7/htslib/cram/thread_pool.o build/temp.linux-x86_64-2.7/htslib/cram/cram_index.o build/temp.linux-x86_64-2.7/htslib/cram/mFILE.o build/temp.linux-x86_64-2.7/htslib/cram/cram_samtools.o build/temp.linux-x86_64-2.7/htslib/cram/pooled_alloc.o build/temp.linux-x86_64-2.7/htslib/cram/open_trace_file.o build/temp.linux-x86_64-2.7/htslib/cram/zfio.o build/temp.linux-x86_64-2.7/htslib/cram/files.o build/temp.linux-x86_64-2.7/htslib/cram/cram_decode.o build/temp.linux-x86_64-2.7/htslib/cram/cram_codecs.o build/temp.linux-x86_64-2.7/htslib/cram/md5.o build/temp.linux-x86_64-2.7/htslib/cram/cram_io.o build/temp.linux-x86_64-2.7/htslib/cram/vlen.o build/temp.linux-x86_64-2.7/htslib/cram/cram_stats.o -Lpysam -lz -o build/lib.linux-x86_64-2.7/pysam/cfaidx.so | |
| warning: no files found matching 'tests/pysam_data' | |
| warning: no files found matching 'tests/tabix_data' | |
| Running setup.py install for ga4gh | |
| Installing ga4gh_client script to /usr/local/google/home/pashields/Envs/ga4gh-pip-install/bin | |
| Installing ga4gh_server script to /usr/local/google/home/pashields/Envs/ga4gh-pip-install/bin | |
| Successfully installed werkzeug wormtable avro pysam requests ga4gh | |
| Cleaning up... | |
| (ga4gh-pip-install)λ pashields ~ → pip install sandboxes/server/dist/ga4gh-0.5.0.tar.gz |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment