sci-biology:pysam-0.12:20170902-145716.log

sci-biology:pysam-0.12:20170902-145716.log (text/plain), 103.21 KB, created by Toralf Förster on 2017-09-02 15:04:04 UTC

 * Package:    sci-biology/pysam-0.12
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux python_targets_python2_7 python_targets_python3_4 userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking pysam-0.12.tar.gz to /var/tmp/portage/sci-biology/pysam-0.12/work
>>> Source unpacked in /var/tmp/portage/sci-biology/pysam-0.12/work
>>> Preparing source in /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12 ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12 ...
>>> Source compiled.
>>> Test phase [not enabled]: sci-biology/pysam-0.12

>>> Install pysam-0.12 into /var/tmp/portage/sci-biology/pysam-0.12/image/ category sci-biology
 * python2_7: running distutils-r1_run_phase distutils-r1_python_install
/usr/bin/python2.7 setup.py install --root=/var/tmp/portage/sci-biology/pysam-0.12/image/_python2.7
checking for gcc... x86_64-pc-linux-gnu-gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking shared library type... plain .so
checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking whether fdatasync is declared... yes
checking for fdatasync... yes
checking for library containing log... -lm
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing connect... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... yes
checking for lzma_easy_buffer_encode in -llzma... yes
configure: WARNING: GCS support not enabled: requires libcurl support
configure: WARNING: S3 support not enabled: requires libcurl support
checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating htslib.pc.tmp
config.status: creating config.h
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is shared
# pysam: HTSLIB_CONFIGURE_OPTIONS=--disable-libcurl
# pysam: htslib configure options: --disable-libcurl
# pysam: htslib_config LIBS=-llzma -lbz2 -lz -lm
# pysam: htslib_config PLATFORM=default
# pysam: htslib_config LIBHTS_OBJS=kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o
# pysam: htslib_config LDFLAGS=-Wl,-O1 -Wl,--as-needed
# pysam: config_option: ENABLE_PLUGINS=0
# pysam: config_option: HAVE_COMMONCRYPTO=0
# pysam: config_option: HAVE_GMTIME_R=1
# pysam: config_option: HAVE_HMAC=0
# pysam: config_option: HAVE_IRODS=0
# pysam: config_option: HAVE_LIBCURL=0
# pysam: config_option: HAVE_MMAP=1
running install
running build
running build_py
creating /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam
copying pysam/version.py -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam
copying pysam/utils.py -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam
copying pysam/samtools.py -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam
copying pysam/namedtuple.py -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam
copying pysam/config.py -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam
copying pysam/bcftools.py -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam
copying pysam/__init__.py -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam
copying pysam/Pileup.py -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam
creating /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include
copying pysam/include/__init__.py -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
package init file 'samtools/win32/__init__.py' not found (or not a regular file)
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)
copying pysam/libcvcf.pxd -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam
copying pysam/libcutils.pxd -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam
copying pysam/libctabixproxies.pxd -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam
copying pysam/libctabix.pxd -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam
copying pysam/libcsamtools.pxd -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam
copying pysam/libcsamfile.pxd -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam
copying pysam/libchtslib.pxd -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam
copying pysam/libcfaidx.pxd -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam
copying pysam/libcbcftools.pxd -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam
copying pysam/libcbcf.pxd -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam
copying pysam/libcalignmentfile.pxd -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam
copying pysam/libcalignedsegment.pxd -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam
copying pysam/tabix_util.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam
copying pysam/samfile_util.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam
copying pysam/pysam_util.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam
copying pysam/pysam_stream.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam
copying pysam/htslib_util.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam
copying pysam/csamtools_util.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam
copying pysam/cbcftools_util.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam
creating /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/samtools
copying samtools/config.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/samtools
copying samtools/version.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/samtools
copying samtools/stats_isize.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/samtools
copying samtools/samtools.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/samtools
copying samtools/sample.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/samtools
copying samtools/sam_opts.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/samtools
copying samtools/sam_header.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/samtools
copying samtools/sam.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/samtools
copying samtools/pysam.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/samtools
copying samtools/bam_plbuf.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/samtools
copying samtools/bam_lpileup.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/samtools
copying samtools/bam_endian.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/samtools
copying samtools/bam2bcf.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/samtools
copying samtools/bam.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/samtools
creating /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/bcftools
copying bcftools/version.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/bcftools
copying bcftools/vcmp.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/bcftools
copying bcftools/vcfbuf.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/bcftools
copying bcftools/regidx.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/bcftools
copying bcftools/rbuf.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/bcftools
copying bcftools/pysam.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/bcftools
copying bcftools/prob1.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/bcftools
copying bcftools/ploidy.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/bcftools
copying bcftools/mw.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/bcftools
copying bcftools/kmin.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/bcftools
copying bcftools/kheap.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/bcftools
copying bcftools/khash_str2str.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/bcftools
copying bcftools/hclust.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/bcftools
copying bcftools/gvcf.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/bcftools
copying bcftools/filter.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/bcftools
copying bcftools/convert.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/bcftools
copying bcftools/call.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/bcftools
copying bcftools/bin.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/bcftools
copying bcftools/bcftools.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/bcftools
copying bcftools/bam_sample.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/bcftools
copying bcftools/bam2bcf.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/bcftools
copying bcftools/HMM.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/bcftools
creating /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/samtools/win32
copying samtools/win32/zlib.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/samtools/win32
copying samtools/win32/zconf.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/samtools/win32
copying samtools/win32/xcurses.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/samtools/win32
creating /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/htslib
copying htslib/config.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/htslib
copying htslib/version.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/htslib
copying htslib/thread_pool_internal.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/htslib
copying htslib/hts_internal.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/htslib
copying htslib/hfile_internal.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/htslib
copying htslib/bcf_sr_sort.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/htslib
creating /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/htslib/htslib
copying htslib/htslib/vcfutils.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/htslib/htslib
copying htslib/htslib/vcf_sweep.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/htslib/htslib
copying htslib/htslib/vcf.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/htslib/htslib
copying htslib/htslib/thread_pool.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/htslib/htslib
copying htslib/htslib/tbx.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/htslib/htslib
copying htslib/htslib/synced_bcf_reader.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/htslib/htslib
copying htslib/htslib/sam.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/htslib/htslib
copying htslib/htslib/regidx.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/htslib/htslib
copying htslib/htslib/kstring.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/htslib/htslib
copying htslib/htslib/ksort.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/htslib/htslib
copying htslib/htslib/kseq.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/htslib/htslib
copying htslib/htslib/knetfile.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/htslib/htslib
copying htslib/htslib/klist.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/htslib/htslib
copying htslib/htslib/khash_str2int.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/htslib/htslib
copying htslib/htslib/khash.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/htslib/htslib
copying htslib/htslib/kfunc.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/htslib/htslib
copying htslib/htslib/kbitset.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/htslib/htslib
copying htslib/htslib/hts_log.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/htslib/htslib
copying htslib/htslib/hts_endian.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/htslib/htslib
copying htslib/htslib/hts_defs.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/htslib/htslib
copying htslib/htslib/hts.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/htslib/htslib
copying htslib/htslib/hfile.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/htslib/htslib
copying htslib/htslib/faidx.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/htslib/htslib
copying htslib/htslib/cram.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/htslib/htslib
copying htslib/htslib/bgzf.h -> /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/include/htslib/htslib
running build_ext
skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
building 'pysam.libchtslib' extension
creating /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7
creating /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libchtslib.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libchtslib.c: In function ‘__pyx_pf_5pysam_10libchtslib_5HFile_6closed___get__’:
pysam/libchtslib.c:2589:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong((__pyx_v_self->fp == NULL)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 84, __pyx_L1_error)
   ^~~~~~~~~
pysam/libchtslib.c:2589:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libchtslib.c: In function ‘__pyx_pf_5pysam_10libchtslib_5HFile_18isatty’:
pysam/libchtslib.c:3721:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(Py_False);
   ^~~~~~~~~~~~
pysam/libchtslib.c: In function ‘__pyx_pf_5pysam_10libchtslib_5HFile_20readable’:
pysam/libchtslib.c:3788:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 148, __pyx_L1_error)
     ^~~~~~~~~
pysam/libchtslib.c:3788:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libchtslib.c:3795:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 148, __pyx_L1_error)
   ^~~~~~~~~
pysam/libchtslib.c:3795:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libchtslib.c: In function ‘__pyx_pf_5pysam_10libchtslib_5HFile_36seekable’:
pysam/libchtslib.c:5486:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong((__pyx_v_self->fp != NULL)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 272, __pyx_L1_error)
   ^~~~~~~~~
pysam/libchtslib.c:5486:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libchtslib.c: In function ‘__pyx_pf_5pysam_10libchtslib_5HFile_40writable’:
pysam/libchtslib.c:5658:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 278, __pyx_L1_error)
     ^~~~~~~~~
pysam/libchtslib.c:5658:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libchtslib.c:5665:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 278, __pyx_L1_error)
   ^~~~~~~~~
pysam/libchtslib.c:5665:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libchtslib.c: In function ‘__pyx_pf_5pysam_10libchtslib_7HTSFile_10__exit__’:
pysam/libchtslib.c:7499:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(Py_False);
   ^~~~~~~~~~~~
pysam/libchtslib.c: In function ‘__pyx_pf_5pysam_10libchtslib_7HTSFile_9is_closed___get__’:
pysam/libchtslib.c:8237:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong((__pyx_v_self->htsfile == NULL)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 427, __pyx_L1_error)
   ^~~~~~~~~
pysam/libchtslib.c:8237:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libchtslib.c: In function ‘__pyx_pf_5pysam_10libchtslib_7HTSFile_6closed___get__’:
pysam/libchtslib.c:8300:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong((__pyx_v_self->htsfile == NULL)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 432, __pyx_L1_error)
   ^~~~~~~~~
pysam/libchtslib.c:8300:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libchtslib.c: In function ‘__pyx_pf_5pysam_10libchtslib_7HTSFile_8is_write___get__’:
pysam/libchtslib.c:8368:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 437, __pyx_L1_error)
     ^~~~~~~~~
pysam/libchtslib.c:8368:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libchtslib.c:8375:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 437, __pyx_L1_error)
   ^~~~~~~~~
pysam/libchtslib.c:8375:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libchtslib.c: In function ‘__pyx_pf_5pysam_10libchtslib_7HTSFile_7is_read___get__’:
pysam/libchtslib.c:8447:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 442, __pyx_L1_error)
     ^~~~~~~~~
pysam/libchtslib.c:8447:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libchtslib.c:8454:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 442, __pyx_L1_error)
   ^~~~~~~~~
pysam/libchtslib.c:8454:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libchtslib.c: In function ‘__pyx_pf_5pysam_10libchtslib_7HTSFile_6is_sam___get__’:
pysam/libchtslib.c:8526:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 447, __pyx_L1_error)
     ^~~~~~~~~
pysam/libchtslib.c:8526:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libchtslib.c:8533:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 447, __pyx_L1_error)
   ^~~~~~~~~
pysam/libchtslib.c:8533:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libchtslib.c: In function ‘__pyx_pf_5pysam_10libchtslib_7HTSFile_6is_bam___get__’:
pysam/libchtslib.c:8605:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 452, __pyx_L1_error)
     ^~~~~~~~~
pysam/libchtslib.c:8605:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libchtslib.c:8612:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 452, __pyx_L1_error)
   ^~~~~~~~~
pysam/libchtslib.c:8612:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libchtslib.c: In function ‘__pyx_pf_5pysam_10libchtslib_7HTSFile_7is_cram___get__’:
pysam/libchtslib.c:8684:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 457, __pyx_L1_error)
     ^~~~~~~~~
pysam/libchtslib.c:8684:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libchtslib.c:8691:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 457, __pyx_L1_error)
   ^~~~~~~~~
pysam/libchtslib.c:8691:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libchtslib.c: In function ‘__pyx_pf_5pysam_10libchtslib_7HTSFile_6is_vcf___get__’:
pysam/libchtslib.c:8763:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 462, __pyx_L1_error)
     ^~~~~~~~~
pysam/libchtslib.c:8763:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libchtslib.c:8770:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 462, __pyx_L1_error)
   ^~~~~~~~~
pysam/libchtslib.c:8770:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libchtslib.c: In function ‘__pyx_pf_5pysam_10libchtslib_7HTSFile_6is_bcf___get__’:
pysam/libchtslib.c:8842:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 467, __pyx_L1_error)
     ^~~~~~~~~
pysam/libchtslib.c:8842:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libchtslib.c:8849:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 467, __pyx_L1_error)
   ^~~~~~~~~
pysam/libchtslib.c:8849:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libchtslib.c: In function ‘__pyx_pf_5pysam_10libchtslib_7HTSFile_9is_stream___get__’:
pysam/libchtslib.c:12056:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_v_self->is_stream); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 2571, __pyx_L1_error)
   ^~~~~~~~~
pysam/libchtslib.c:12056:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libchtslib.c: In function ‘__pyx_pf_5pysam_10libchtslib_7HTSFile_9is_remote___get__’:
pysam/libchtslib.c:12103:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_v_self->is_remote); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 2572, __pyx_L1_error)
   ^~~~~~~~~
pysam/libchtslib.c:12103:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libchtslib.c: In function ‘__pyx_pf_5pysam_10libchtslib_7HTSFile_20duplicate_filehandle___get__’:
pysam/libchtslib.c:12150:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_v_self->duplicate_filehandle); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 2573, __pyx_L1_error)
   ^~~~~~~~~
pysam/libchtslib.c:12150:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -O2 -pipe -march=native -Wall /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/libchtslib.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/htslib_util.o -L/usr/lib64 -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/usr/lib64 -lz -lhts -lpython2.7 -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/libchtslib.so
skipping 'pysam/libcsamfile.c' Cython extension (up-to-date)
building 'pysam.libcsamfile' extension
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcsamfile.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -O2 -pipe -march=native -Wall /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/libcsamfile.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/htslib_util.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/samfile_util.o -L/usr/lib64 -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/usr/lib64 -lz -lhts -lchtslib -lpython2.7 -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/libcsamfile.so
skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date)
building 'pysam.libcalignmentfile' extension
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/libcalignmentfile.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_2has_index’:
pysam/libcalignmentfile.c:6725:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong((__pyx_v_self->index != NULL)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 454, __pyx_L1_error)
   ^~~~~~~~~
pysam/libcalignmentfile.c:6725:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_4check_index’:
pysam/libcalignmentfile.c:6908:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(Py_True);
   ^~~~~~~~~~~~
pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_14fetch’:
pysam/libcalignmentfile.c:10521:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __Pyx_INCREF(Py_False);
     ^~~~~~~~~~~~
pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_26find_introns’:
pysam/libcalignmentfile.c:14095:7: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
       __Pyx_INCREF(Py_False);
       ^~~~~~~~~~~~
pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_36__exit__’:
pysam/libcalignmentfile.c:15493:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(Py_False);
   ^~~~~~~~~~~~
pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6header___get__’:
pysam/libcalignmentfile.c:17620:11: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
           __Pyx_INCREF(((PyObject *)(&PyString_Type)));
           ^~~~~~~~~~~~
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’:
pysam/libcalignmentfile.c:23498:21: warning: assignment discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
   __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));
                     ^
pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_7SNPCall___str__’:
pysam/libcalignmentfile.c:26115:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_12IndexedReads_2build’:
pysam/libcalignmentfile.c:26560:7: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
       __Pyx_INCREF(((PyObject *)(&PyList_Type)));
       ^~~~~~~~~~~~
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’:
pysam/libcalignmentfile.c:22054:9: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
         bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0);
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcalignmentfile.c: In function ‘__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open’:
pysam/libcalignmentfile.c:8531:13: warning: ignoring return value of ‘sam_hdr_write’, declared with attribute warn_unused_result [-Wunused-result]
             sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Ipysam -Isamtools -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -O2 -pipe -march=native -Wall /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/libcalignmentfile.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/htslib_util.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/samfile_util.o -L/usr/lib64 -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/usr/lib64 -lz -lhts -lchtslib -lpython2.7 -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/libcalignmentfile.so
skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date)
building 'pysam.libcalignedsegment' extension
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcalignedsegment.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignedsegment.c: In function ‘__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_4__str__’:
pysam/libcalignedsegment.c:10438:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
pysam/libcalignedsegment.c: In function ‘__pyx_f_5pysam_18libcalignedsegment_14AlignedSegment_has_tag’:
pysam/libcalignedsegment.c:22482:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong((__pyx_v_v != NULL)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 2018, __pyx_L1_error)
   ^~~~~~~~~
pysam/libcalignedsegment.c:22482:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libcalignedsegment.c: In function ‘__pyx_pf_5pysam_18libcalignedsegment_12PileupColumn_2__str__’:
pysam/libcalignedsegment.c:28091:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
pysam/libcalignedsegment.c:28126:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
pysam/libcalignedsegment.c: In function ‘__pyx_pf_5pysam_18libcalignedsegment_10PileupRead_2__str__’:
pysam/libcalignedsegment.c:29294:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
pysam/libcalignedsegment.c: In function ‘__pyx_array_get_memview’:
pysam/libcalignedsegment.c:32776:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_self->dtype_is_object); if (unlikely(!__pyx_t_2)) __PYX_ERR(2, 226, __pyx_L1_error)
   ^~~~~~~~~
pysam/libcalignedsegment.c:32776:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libcalignedsegment.c: In function ‘__pyx_memoryview_is_slice’:
pysam/libcalignedsegment.c:34603:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
         __pyx_t_7 = __Pyx_PyBool_FromLong(__pyx_v_self->dtype_is_object); if (unlikely(!__pyx_t_7)) __PYX_ERR(2, 424, __pyx_L4_error)
         ^~~~~~~~~
pysam/libcalignedsegment.c:34603:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libcalignedsegment.c: In function ‘__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_16is_c_contig’:
pysam/libcalignedsegment.c:37117:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_memviewslice_is_contig((__pyx_v_mslice[0]), 'C', __pyx_v_self->view.ndim)); if (unlikely(!__pyx_t_1)) __PYX_ERR(2, 609, __pyx_L1_error)
   ^~~~~~~~~
pysam/libcalignedsegment.c:37117:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libcalignedsegment.c: In function ‘__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_18is_f_contig’:
pysam/libcalignedsegment.c:37191:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_memviewslice_is_contig((__pyx_v_mslice[0]), 'F', __pyx_v_self->view.ndim)); if (unlikely(!__pyx_t_1)) __PYX_ERR(2, 615, __pyx_L1_error)
   ^~~~~~~~~
pysam/libcalignedsegment.c:37191:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libcalignedsegment.c: In function ‘__pyx_memoryview_new’:
pysam/libcalignedsegment.c:37434:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_dtype_is_object); if (unlikely(!__pyx_t_2)) __PYX_ERR(2, 644, __pyx_L1_error)
   ^~~~~~~~~
pysam/libcalignedsegment.c:37434:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libcalignedsegment.c: In function ‘_unellipsify’:
pysam/libcalignedsegment.c:37952:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __pyx_t_4 = __Pyx_PyBool_FromLong(__pyx_v_have_slices); if (unlikely(!__pyx_t_4)) __PYX_ERR(2, 684, __pyx_L1_error)
     ^~~~~~~~~
pysam/libcalignedsegment.c:37952:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libcalignedsegment.c: In function ‘__pyx_memoryview_fromslice’:
pysam/libcalignedsegment.c:40291:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_dtype_is_object); if (unlikely(!__pyx_t_2)) __PYX_ERR(2, 999, __pyx_L1_error)
   ^~~~~~~~~
pysam/libcalignedsegment.c:40291:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libcalignedsegment.c: In function ‘initlibcalignedsegment’:
pysam/libcalignedsegment.c:47348:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __Pyx_INCREF(((PyObject *)(&PyDict_Type)));
     ^~~~~~~~~~~~
pysam/libcalignedsegment.c:47364:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyInt_Type)));
   ^~~~~~~~~~~~
pysam/libcalignedsegment.c: In function ‘__Pyx_PyInt_EqObjC’:
pysam/libcalignedsegment.c:51495:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
         Py_RETURN_TRUE;
         ^~~~~~~~~~~~~~
pysam/libcalignedsegment.c:51502:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             Py_RETURN_TRUE;
             ^~~~~~~~~~~~~~
pysam/libcalignedsegment.c:51504:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             Py_RETURN_FALSE;
             ^~~~~~~~~~~~~~~
pysam/libcalignedsegment.c:51552:17: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                 default: Py_RETURN_FALSE;
                 ^~~~~~~
pysam/libcalignedsegment.c:51557:17: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                 Py_RETURN_TRUE;
                 ^~~~~~~~~~~~~~
pysam/libcalignedsegment.c:51559:17: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                 Py_RETURN_FALSE;
                 ^~~~~~~~~~~~~~~
pysam/libcalignedsegment.c:51567:17: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                 Py_RETURN_TRUE;
                 ^~~~~~~~~~~~~~
pysam/libcalignedsegment.c:51569:17: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                 Py_RETURN_FALSE;
                 ^~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/htslib_util.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Ipysam -Isamtools -I. -I/usr/include -I/usr/include/python2.7 -c pysam/samfile_util.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/samfile_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -O2 -pipe -march=native -Wall /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/libcalignedsegment.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/htslib_util.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/samfile_util.o -L/usr/lib64 -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/usr/lib64 -lz -lhts -lchtslib -lpython2.7 -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/libcalignedsegment.so
skipping 'pysam/libctabix.c' Cython extension (up-to-date)
building 'pysam.libctabix' extension
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libctabix.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__’:
pysam/libctabix.c:6105:27: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
         __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
                           ^
pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_2tabix_index’:
pysam/libctabix.c:10303:39: warning: overflow in implicit constant conversion [-Woverflow]
   __pyx_t_8 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_8)) __PYX_ERR(0, 918, __pyx_L1_error)
                                       ^~~~~~~~
pysam/libctabix.c:10335:39: warning: overflow in implicit constant conversion [-Woverflow]
   __pyx_t_4 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 919, __pyx_L1_error)
                                       ^~~~~~~~
pysam/libctabix.c:10637:43: warning: overflow in implicit constant conversion [-Woverflow]
       __pyx_t_4 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_4)) __PYX_ERR(0, 943, __pyx_L1_error)
                                           ^~~~~~~~
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/tabix_util.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/tabix_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -O2 -pipe -march=native -Wall /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/libctabix.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/tabix_util.o -Lpysam -L/usr/lib64 -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/usr/lib64 -lz -lhts -lchtslib -lpython2.7 -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/libctabix.so
skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date)
building 'pysam.libctabixproxies' extension
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -I/usr/include/python2.7 -c pysam/libctabixproxies.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libctabixproxies.c: In function ‘initlibctabixproxies’:
pysam/libctabixproxies.c:18082:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
pysam/libctabixproxies.c:18085:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
pysam/libctabixproxies.c:18112:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
pysam/libctabixproxies.c:18140:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
pysam/libctabixproxies.c:18194:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyInt_Type)));
   ^~~~~~~~~~~~
pysam/libctabixproxies.c:18197:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyInt_Type)));
   ^~~~~~~~~~~~
pysam/libctabixproxies.c:18254:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
pysam/libctabixproxies.c:18308:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
pysam/libctabixproxies.c:18311:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
pysam/libctabixproxies.c:18342:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
pysam/libctabixproxies.c:18360:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyInt_Type)));
   ^~~~~~~~~~~~
pysam/libctabixproxies.c:18378:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyInt_Type)));
   ^~~~~~~~~~~~
pysam/libctabixproxies.c:18396:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
pysam/libctabixproxies.c:18414:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyFloat_Type)));
   ^~~~~~~~~~~~
pysam/libctabixproxies.c:18432:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
pysam/libctabixproxies.c:18450:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyInt_Type)));
   ^~~~~~~~~~~~
pysam/libctabixproxies.c:18468:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyInt_Type)));
   ^~~~~~~~~~~~
pysam/libctabixproxies.c:18486:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
pysam/libctabixproxies.c:18504:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyInt_Type)));
   ^~~~~~~~~~~~
pysam/libctabixproxies.c:18522:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
pysam/libctabixproxies.c:18540:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
pysam/libctabixproxies.c:18563:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
pysam/libctabixproxies.c:18581:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyInt_Type)));
   ^~~~~~~~~~~~
pysam/libctabixproxies.c:18599:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
pysam/libctabixproxies.c:18617:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
pysam/libctabixproxies.c:18635:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
pysam/libctabixproxies.c:18653:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
pysam/libctabixproxies.c:18671:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
pysam/libctabixproxies.c:18689:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
pysam/libctabixproxies.c:18707:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
pysam/libctabixproxies.c: In function ‘__Pyx_PyInt_EqObjC’:
pysam/libctabixproxies.c:19408:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
         Py_RETURN_TRUE;
         ^~~~~~~~~~~~~~
pysam/libctabixproxies.c:19415:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             Py_RETURN_TRUE;
             ^~~~~~~~~~~~~~
pysam/libctabixproxies.c:19417:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             Py_RETURN_FALSE;
             ^~~~~~~~~~~~~~~
pysam/libctabixproxies.c:19465:17: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                 default: Py_RETURN_FALSE;
                 ^~~~~~~
pysam/libctabixproxies.c:19470:17: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                 Py_RETURN_TRUE;
                 ^~~~~~~~~~~~~~
pysam/libctabixproxies.c:19472:17: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                 Py_RETURN_FALSE;
                 ^~~~~~~~~~~~~~~
pysam/libctabixproxies.c:19480:17: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                 Py_RETURN_TRUE;
                 ^~~~~~~~~~~~~~
pysam/libctabixproxies.c:19482:17: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                 Py_RETURN_FALSE;
                 ^~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -O2 -pipe -march=native -Wall /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/libctabixproxies.o -L/usr/lib64 -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/usr/lib64 -lz -lhts -lchtslib -lpython2.7 -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/libctabixproxies.so
skipping 'pysam/libcvcf.c' Cython extension (up-to-date)
building 'pysam.libcvcf' extension
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcvcf.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_12format_formatdata’:
pysam/libcvcf.c:12683:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
         __Pyx_INCREF(((PyObject *)(&PyString_Type)));
         ^~~~~~~~~~~~
pysam/libcvcf.c:12762:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
         __Pyx_INCREF(((PyObject *)(&PyString_Type)));
         ^~~~~~~~~~~~
pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_26convertGTback’:
pysam/libcvcf.c:16909:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)(&PyString_Type)));
   ^~~~~~~~~~~~
pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_28parse_formatdata’:
pysam/libcvcf.c:18148:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
         __Pyx_INCREF(((PyObject *)(&PyFloat_Type)));
         ^~~~~~~~~~~~
pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_30inregion’:
pysam/libcvcf.c:18543:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __Pyx_INCREF(Py_True);
     ^~~~~~~~~~~~
pysam/libcvcf.c:18635:7: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
       __Pyx_INCREF(Py_True);
       ^~~~~~~~~~~~
pysam/libcvcf.c:18659:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(Py_False);
   ^~~~~~~~~~~~
pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_77compare_calls’:
pysam/libcvcf.c:28692:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __Pyx_INCREF(Py_False);
     ^~~~~~~~~~~~
pysam/libcvcf.c: In function ‘__Pyx_PyInt_EqObjC’:
pysam/libcvcf.c:34875:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
         Py_RETURN_TRUE;
         ^~~~~~~~~~~~~~
pysam/libcvcf.c:34882:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             Py_RETURN_TRUE;
             ^~~~~~~~~~~~~~
pysam/libcvcf.c:34884:13: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
             Py_RETURN_FALSE;
             ^~~~~~~~~~~~~~~
pysam/libcvcf.c:34932:17: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                 default: Py_RETURN_FALSE;
                 ^~~~~~~
pysam/libcvcf.c:34937:17: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                 Py_RETURN_TRUE;
                 ^~~~~~~~~~~~~~
pysam/libcvcf.c:34939:17: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                 Py_RETURN_FALSE;
                 ^~~~~~~~~~~~~~~
pysam/libcvcf.c:34947:17: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                 Py_RETURN_TRUE;
                 ^~~~~~~~~~~~~~
pysam/libcvcf.c:34949:17: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
                 Py_RETURN_FALSE;
                 ^~~~~~~~~~~~~~~
pysam/libcvcf.c: In function ‘__pyx_pf_5pysam_7libcvcf_3VCF_32parse_data.isra.65’:
pysam/libcvcf.c:24041:16: warning: ‘__pyx_v_qual’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   __pyx_t_10 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_10)) __PYX_ERR(0, 873, __pyx_L1_error)
                ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -O2 -pipe -march=native -Wall /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/libcvcf.o -L/usr/lib64 -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/usr/lib64 -lz -lhts -lchtslib -lpython2.7 -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/libcvcf.so
skipping 'pysam/libcbcf.c' Cython extension (up-to-date)
building 'pysam.libcbcf' extension
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcbcf.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcbcf.c: In function ‘__pyx_f_5pysam_7libcbcf_bcf_info_get_value’:
pysam/libcbcf.c:8675:7: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
       __Pyx_INCREF(Py_True);
       ^~~~~~~~~~~~
pysam/libcbcf.c: In function ‘__pyx_f_5pysam_7libcbcf_bcf_format_set_value’:
pysam/libcbcf.c:12571:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __pyx_t_3 = __Pyx_PyBool_FromLong((!(!__pyx_t_2))); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 813, __pyx_L1_error)
     ^~~~~~~~~
pysam/libcbcf.c:12571:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libcbcf.c: In function ‘__pyx_f_5pysam_7libcbcf_bcf_sample_set_phased’:
pysam/libcbcf.c:16321:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
         __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_v_phased); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1155, __pyx_L1_error)
         ^~~~~~~~~
pysam/libcbcf.c:16321:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_12__str__’:
pysam/libcbcf.c:30545:3: warning: ‘bcf_hdr_fmt_text’ is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations]
   __pyx_v_hstr = bcf_hdr_fmt_text(__pyx_v_self->ptr, 0, (&__pyx_v_hlen));
   ^~~~~~~~~~~~
In file included from pysam/htslib_util.h:5:0,
                 from pysam/libcbcf.c:439:
htslib/htslib/vcf.h:439:11: note: declared here
     char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len)
           ^~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_19VariantRecordFilter_35__richcmp__’:
pysam/libcbcf.c:35380:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_6 = __Pyx_PyBool_FromLong(__pyx_v_cmp); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 2319, __pyx_L1_error)
   ^~~~~~~~~
pysam/libcbcf.c:35380:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_17VariantRecordInfo_6__getitem__’:
pysam/libcbcf.c:38547:7: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
       __pyx_t_9 = __Pyx_PyBool_FromLong(__pyx_t_3); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 2540, __pyx_L1_error)
       ^~~~~~~~~
pysam/libcbcf.c:38547:7: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libcbcf.c:38554:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __pyx_t_9 = __Pyx_PyBool_FromLong(__pyx_t_3); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 2540, __pyx_L1_error)
     ^~~~~~~~~
pysam/libcbcf.c:38554:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_17VariantRecordInfo_17get’:
pysam/libcbcf.c:40080:7: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
       __pyx_t_9 = __Pyx_PyBool_FromLong(__pyx_t_3); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 2650, __pyx_L1_error)
       ^~~~~~~~~
pysam/libcbcf.c:40080:7: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libcbcf.c:40087:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __pyx_t_9 = __Pyx_PyBool_FromLong(__pyx_t_3); if (unlikely(!__pyx_t_9)) __PYX_ERR(0, 2650, __pyx_L1_error)
     ^~~~~~~~~
pysam/libcbcf.c:40087:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_17VariantRecordInfo_39__richcmp__’:
pysam/libcbcf.c:42395:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_v_cmp); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 2790, __pyx_L1_error)
   ^~~~~~~~~
pysam/libcbcf.c:42395:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_20VariantRecordSamples_33__richcmp__’:
pysam/libcbcf.c:45166:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_6 = __Pyx_PyBool_FromLong(__pyx_v_cmp); if (unlikely(!__pyx_t_6)) __PYX_ERR(0, 2939, __pyx_L1_error)
   ^~~~~~~~~
pysam/libcbcf.c:45166:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantRecord_8__richcmp__’:
pysam/libcbcf.c:49809:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_5 = __Pyx_PyBool_FromLong(__pyx_v_cmp); if (unlikely(!__pyx_t_5)) __PYX_ERR(0, 3268, __pyx_L1_error)
   ^~~~~~~~~
pysam/libcbcf.c:49809:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_19VariantRecordSample_6phased___get__’:
pysam/libcbcf.c:51090:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_f_5pysam_7libcbcf_bcf_sample_get_phased(__pyx_v_self)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 3387, __pyx_L1_error)
   ^~~~~~~~~
pysam/libcbcf.c:51090:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_19VariantRecordSample_39__richcmp__’:
pysam/libcbcf.c:53851:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_cmp); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 3522, __pyx_L1_error)
   ^~~~~~~~~
pysam/libcbcf.c:53851:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_18is_valid_tid’:
pysam/libcbcf.c:64237:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_t_3); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 4257, __pyx_L1_error)
   ^~~~~~~~~
pysam/libcbcf.c:64237:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_12drop_samples___get__’:
pysam/libcbcf.c:66207:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_v_self->drop_samples); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 135, __pyx_L1_error)
   ^~~~~~~~~
pysam/libcbcf.c:66207:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_10is_reading___get__’:
pysam/libcbcf.c:66254:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_v_self->is_reading); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 138, __pyx_L1_error)
   ^~~~~~~~~
pysam/libcbcf.c:66254:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_14header_written___get__’:
pysam/libcbcf.c:66301:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_v_self->header_written); if (unlikely(!__pyx_t_1)) __PYX_ERR(1, 139, __pyx_L1_error)
   ^~~~~~~~~
pysam/libcbcf.c:66301:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -O2 -pipe -march=native -Wall /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/libcbcf.o -L/usr/lib64 -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/usr/lib64 -lz -lhts -lchtslib -lpython2.7 -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/libcbcf.so
skipping 'pysam/libcbgzf.c' Cython extension (up-to-date)
building 'pysam.libcbgzf' extension
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Ihtslib -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcbgzf.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcbgzf.c: In function ‘__pyx_pf_5pysam_8libcbgzf_7BGZFile_6closed___get__’:
pysam/libcbgzf.c:2838:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong((__pyx_v_self->bgzf == NULL)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 125, __pyx_L1_error)
   ^~~~~~~~~
pysam/libcbgzf.c:2838:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libcbgzf.c: In function ‘__pyx_pf_5pysam_8libcbgzf_7BGZFile_20readable’:
pysam/libcbgzf.c:3667:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 177, __pyx_L1_error)
     ^~~~~~~~~
pysam/libcbgzf.c:3667:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libcbgzf.c:3674:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_1); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 177, __pyx_L1_error)
   ^~~~~~~~~
pysam/libcbgzf.c:3674:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libcbgzf.c: In function ‘__pyx_pf_5pysam_8libcbgzf_7BGZFile_22writable’:
pysam/libcbgzf.c:3743:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_t_2); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 180, __pyx_L1_error)
     ^~~~~~~~~
pysam/libcbgzf.c:3743:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libcbgzf.c: In function ‘__pyx_pf_5pysam_8libcbgzf_7BGZFile_24seekable’:
pysam/libcbgzf.c:3812:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(Py_True);
   ^~~~~~~~~~~~
x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -O2 -pipe -march=native -Wall /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/libcbgzf.o -L/usr/lib64 -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/usr/lib64 -lz -lhts -lchtslib -lpython2.7 -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/libcbgzf.so
skipping 'pysam/libcfaidx.c' Cython extension (up-to-date)
building 'pysam.libcfaidx' extension
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcfaidx.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcfaidx.c: In function ‘__pyx_pf_5pysam_9libcfaidx_9FastaFile_2is_open’:
pysam/libcfaidx.c:2254:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong((__pyx_v_self->fastafile != NULL)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 123, __pyx_L1_error)
   ^~~~~~~~~
pysam/libcfaidx.c:2254:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libcfaidx.c: In function ‘__pyx_pf_5pysam_9libcfaidx_9FastaFile_14__exit__’:
pysam/libcfaidx.c:3295:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(Py_False);
   ^~~~~~~~~~~~
pysam/libcfaidx.c: In function ‘__pyx_pf_5pysam_9libcfaidx_9FastaFile_6closed___get__’:
pysam/libcfaidx.c:3383:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong((!__pyx_t_4)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 198, __pyx_L1_error)
   ^~~~~~~~~
pysam/libcfaidx.c:3383:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libcfaidx.c: In function ‘__pyx_pf_5pysam_9libcfaidx_9FastxFile_2is_open’:
pysam/libcfaidx.c:7868:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong((__pyx_v_self->entry != NULL)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 522, __pyx_L1_error)
   ^~~~~~~~~
pysam/libcfaidx.c:7868:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
pysam/libcfaidx.c: In function ‘__pyx_pf_5pysam_9libcfaidx_9FastxFile_12__exit__’:
pysam/libcfaidx.c:8699:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(Py_False);
   ^~~~~~~~~~~~
pysam/libcfaidx.c: In function ‘__pyx_pf_5pysam_9libcfaidx_9FastxFile_6closed___get__’:
pysam/libcfaidx.c:8787:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong((!__pyx_t_4)); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 585, __pyx_L1_error)
   ^~~~~~~~~
pysam/libcfaidx.c:8787:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -O2 -pipe -march=native -Wall /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/libcfaidx.o -Lpysam -L/usr/lib64 -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/usr/lib64 -lz -lhts -lchtslib -lpython2.7 -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/libcfaidx.so
skipping 'pysam/libcsamtools.c' Cython extension (up-to-date)
building 'pysam.libcsamtools' extension
creating /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcsamtools.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/stats_isize.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/stats.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sample.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam_view.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam_utils.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam_opts.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam_header.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/sam_header.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/sam.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/phase.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/padding.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/faidx.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/dict.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/cut_target.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bedidx.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bedcov.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bamtk.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bamshuf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_stat.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_split.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_sort.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_rmdupse.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_rmdup.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_reheader.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_quickcheck.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_plcmd.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_plbuf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_md.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_mate.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_lpileup.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_index.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_import.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_flags.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_color.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_cat.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_aux.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam_addrprg.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam2depth.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam2bcf_indel.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam2bcf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Isamtools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c samtools/bam.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
samtools/bam.c.pysam.c: In function ‘bam_view1’:
samtools/bam.c.pysam.c:54:60: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
     if (fputs(s, pysam_stdout) & fputc('\n', pysam_stdout) != EOF) ret = 0;
                                                            ^
x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -O2 -pipe -march=native -Wall /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/libcsamtools.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/stats_isize.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/stats.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/sample.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/sam_view.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/sam_utils.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/sam_opts.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/sam_header.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/sam.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/phase.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/padding.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/faidx.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/dict.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/cut_target.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bedidx.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bedcov.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bamtk.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bamshuf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_stat.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_split.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_sort.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_rmdupse.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_rmdup.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_reheader.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_quickcheck.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_plcmd.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_plbuf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_md.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_mate.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_lpileup.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_index.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_import.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_flags.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_color.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_cat.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_aux.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam_addrprg.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam2depth.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam2bcf_indel.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam2bcf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/samtools/bam.c.pysam.o -Lpysam -L/usr/lib64 -L/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam -L/usr/lib64 -lz -lhts -lchtslib -lpython2.7 -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/lib/pysam/libcsamtools.so
skipping 'pysam/libcbcftools.c' Cython extension (up-to-date)
building 'pysam.libcbcftools' extension
creating /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/bcftools
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c pysam/libcbcftools.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/version.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcmp.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfview.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfstats.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfsom.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfroh.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfquery.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -Wall -fPIC -Ibcftools -Ipysam -I. -I/usr/include -I/usr/include/python2.7 -c bcftools/vcfplugin.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12-python2_7/temp.linux-x86_64-2.7/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
bcftools/vcfplugin.c.pysam.c:27:20: fatal error: config.h: No such file or directory
 #include "config.h"
                    ^
compilation terminated.
error: command 'x86_64-pc-linux-gnu-gcc' failed with exit status 1
 * ERROR: sci-biology/pysam-0.12::gentoo failed (install phase):
 *   (no error message)
 * 
 * Call stack:
 *     ebuild.sh, line  115:  Called src_install
 *   environment, line 2680:  Called distutils-r1_src_install
 *   environment, line  822:  Called _distutils-r1_run_foreach_impl 'distutils-r1_python_install'
 *   environment, line  314:  Called python_foreach_impl 'distutils-r1_run_phase' 'distutils-r1_python_install'
 *   environment, line 2207:  Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_install'
 *   environment, line 1513:  Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_install'
 *   environment, line 1511:  Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'distutils-r1_python_install'
 *   environment, line  529:  Called distutils-r1_run_phase 'distutils-r1_python_install'
 *   environment, line  790:  Called distutils-r1_python_install
 *   environment, line  706:  Called esetup.py 'install' '--root=/var/tmp/portage/sci-biology/pysam-0.12/image/_python2.7'
 *   environment, line 1058:  Called die
 * The specific snippet of code:
 *       "${@}" || die "${die_args[@]}";
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/pysam-0.12::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/pysam-0.12::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:pysam-0.12:20170902-145716.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/pysam-0.12/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/pysam-0.12/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12'
 * S: '/var/tmp/portage/sci-biology/pysam-0.12/work/pysam-0.12'