sci-biology:pysam-0.16.0.1:20210909-071245.log

sci-biology:pysam-0.16.0.1:20210909-071245.log (text/plain), 173.90 KB, created by Toralf Förster on 2021-09-09 07:20:33 UTC

 * Package:    sci-biology/pysam-0.16.0.1
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux python_targets_python3_9 userland_GNU
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox

>>> Unpacking source...
>>> Unpacking pysam-0.16.0.1.tar.gz to /var/tmp/portage/sci-biology/pysam-0.16.0.1/work
>>> Source unpacked in /var/tmp/portage/sci-biology/pysam-0.16.0.1/work
>>> Preparing source in /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1 ...
 * Applying pysam-0.16.0.1-fix-tests.patch ...
 [ ok ]
 * Will copy sources from /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1
 * python3_9: copying to /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1 ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1 ...
 * python3_9: running distutils-r1_run_phase python_compile
python3.9 setup.py build -j 1
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running build
running build_py
creating /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam
copying pysam/config.py -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam
copying pysam/version.py -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam
copying pysam/utils.py -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam
copying pysam/samtools.py -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam
copying pysam/bcftools.py -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam
copying pysam/__init__.py -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam
copying pysam/Pileup.py -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam
creating /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include
copying pysam/include/__init__.py -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/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)
copying pysam/libcvcf.pxd -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam
copying pysam/libcutils.pxd -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam
copying pysam/libctabixproxies.pxd -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam
copying pysam/libctabix.pxd -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam
copying pysam/libcsamtools.pxd -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam
copying pysam/libcsamfile.pxd -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam
copying pysam/libchtslib.pxd -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam
copying pysam/libcfaidx.pxd -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam
copying pysam/libcbcftools.pxd -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam
copying pysam/libcbcf.pxd -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam
copying pysam/libcalignmentfile.pxd -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam
copying pysam/libcalignedsegment.pxd -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam
copying pysam/version.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam
copying pysam/pysam_util.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam
copying pysam/pysam_stream.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam
copying pysam/htslib_util.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam
copying pysam/csamtools_util.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam
copying pysam/cbcftools_util.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam
creating /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/samtools
copying samtools/config.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/samtools
copying samtools/tmp_file.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/samtools
copying samtools/stats_isize.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/samtools
copying samtools/samtools.pysam.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/samtools
copying samtools/samtools.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/samtools
copying samtools/sample.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/samtools
copying samtools/sam_opts.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/samtools
copying samtools/sam.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/samtools
copying samtools/bedidx.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/samtools
copying samtools/bam_plbuf.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/samtools
copying samtools/bam_lpileup.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/samtools
copying samtools/bam_endian.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/samtools
copying samtools/bam2bcf.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/samtools
copying samtools/bam.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/samtools
creating /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools
copying bcftools/config.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools
copying bcftools/vcmp.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools
copying bcftools/vcfbuf.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools
copying bcftools/variantkey.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools
copying bcftools/regidx.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools
copying bcftools/rbuf.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools
copying bcftools/prob1.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools
copying bcftools/ploidy.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools
copying bcftools/mw.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools
copying bcftools/kmin.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools
copying bcftools/kheap.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools
copying bcftools/khash_str2str.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools
copying bcftools/hex.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools
copying bcftools/hclust.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools
copying bcftools/gvcf.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools
copying bcftools/filter.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools
copying bcftools/convert.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools
copying bcftools/cols.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools
copying bcftools/call.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools
copying bcftools/bin.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools
copying bcftools/bcftools.pysam.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools
copying bcftools/bcftools.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools
copying bcftools/bam_sample.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools
copying bcftools/bam2bcf.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools
copying bcftools/HMM.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools
/usr/lib/python3.9/site-packages/setuptools/lib2to3_ex.py:36: SetuptoolsDeprecationWarning: 2to3 support is deprecated. If the project still requires Python 2 support, please migrate to a single-codebase solution or employ an independent conversion process.
  warnings.warn(
Fixing /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/config.py /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/version.py /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/utils.py /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/samtools.py /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/bcftools.py /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/__init__.py /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/Pileup.py /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/__init__.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
Fixing /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/config.py /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/version.py /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/utils.py /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/samtools.py /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/bcftools.py /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/__init__.py /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/Pileup.py /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/__init__.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
warning: build_py: byte-compiling is disabled, skipping.

running build_ext
cythoning pysam/libchtslib.pyx to pysam/libchtslib.c
/usr/lib/python3.9/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam/libchtslib.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcsamtools.pyx to pysam/libcsamtools.c
/usr/lib/python3.9/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam/libcsamtools.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcbcftools.pyx to pysam/libcbcftools.c
/usr/lib/python3.9/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam/libcbcftools.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcutils.pyx to pysam/libcutils.c
/usr/lib/python3.9/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam/libcutils.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c
/usr/lib/python3.9/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam/libcalignmentfile.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
warning: pysam/libcalignmentfile.pyx:2551:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2556:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2561:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2600:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2605:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
warning: pysam/libcalignmentfile.pyx:2610:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
cythoning pysam/libcsamfile.pyx to pysam/libcsamfile.c
/usr/lib/python3.9/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam/libcsamfile.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcalignedsegment.pyx to pysam/libcalignedsegment.c
/usr/lib/python3.9/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam/libcalignedsegment.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libctabix.pyx to pysam/libctabix.c
/usr/lib/python3.9/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam/libctabix.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcfaidx.pyx to pysam/libcfaidx.c
/usr/lib/python3.9/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam/libcfaidx.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcbcf.pyx to pysam/libcbcf.c
/usr/lib/python3.9/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam/libcbcf.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcbgzf.pyx to pysam/libcbgzf.c
/usr/lib/python3.9/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam/libcbgzf.pyx
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libctabixproxies.pyx to pysam/libctabixproxies.c
/usr/lib/python3.9/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam/libctabixproxies.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
cythoning pysam/libcvcf.pyx to pysam/libcvcf.c
/usr/lib/python3.9/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam/libcvcf.pxd
  tree = Parsing.p_module(s, pxd, full_module_name)
warning: pysam/libcvcf.pyx:1083:27: Unreachable code
building 'pysam.libchtslib' extension
creating /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9
creating /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/pysam
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c pysam/htslib_util.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c pysam/libchtslib.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/pysam/libchtslib.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 -Wl,--defsym=__gentoo_check_ldflags__=0 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/pysam/htslib_util.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/pysam/libchtslib.o -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -L/usr/lib64 -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/usr/lib64 -lz -lhts -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libchtslib.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcsamtools' extension
creating /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools
creating /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/lz4
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c pysam/libcsamtools.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/bam.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/bam2bcf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/bam2bcf_indel.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
samtools/bam2bcf_indel.c.pysam.c: In function ‘bcf_call_gap_prep’:
samtools/bam2bcf_indel.c.pysam.c:413:26: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  413 |                     qq = calloc(qend - qbeg, 1);
      |                          ^~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/htslib/kstring.h:30,
                 from /usr/include/htslib/vcf.h:41,
                 from samtools/bam2bcf.h:31,
                 from samtools/bam2bcf_indel.c.pysam.c:35:
/usr/include/stdlib.h:542:14: note: in a call to allocation function ‘calloc’ declared here
  542 | extern void *calloc (size_t __nmemb, size_t __size)
      |              ^~~~~~
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/bam2depth.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/bam_addrprg.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/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 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/bam_aux.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/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 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/bam_cat.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/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 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/bam_color.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/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 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/bam_fastq.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/bam_flags.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/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 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/bam_index.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/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 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/bam_lpileup.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/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 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/bam_markdup.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/bam_mate.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/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 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/bam_md.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/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 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/bam_plbuf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/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 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/bam_plcmd.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/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 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/bam_quickcheck.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/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 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/bam_reheader.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/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 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/bam_rmdup.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/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 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/bam_rmdupse.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/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 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/bam_sort.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/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 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/bam_split.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/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 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/bam_stat.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/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 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/bamshuf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/bamtk.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/bedcov.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/bedidx.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/coverage.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/cut_target.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/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 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/dict.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/faidx.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/lz4/lz4.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/padding.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/phase.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/sam.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/sam_opts.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/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 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/sam_utils.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/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 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/sam_view.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/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 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/sample.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/samtools.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/stats.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/stats_isize.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/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 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c samtools/tmp_file.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/tmp_file.c.pysam.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 -Wl,--defsym=__gentoo_check_ldflags__=0 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/pysam/libcsamtools.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bam.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bam2bcf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bam2bcf_indel.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bam2depth.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_addrprg.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_aux.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_cat.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_color.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_fastq.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_flags.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_index.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_lpileup.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_markdup.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_mate.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_md.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_plbuf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_plcmd.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_quickcheck.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_reheader.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_rmdup.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_rmdupse.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_sort.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_split.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bam_stat.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bamshuf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bamtk.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bedcov.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/bedidx.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/coverage.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/cut_target.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/dict.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/faidx.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/lz4/lz4.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/padding.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/phase.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/sam.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/sam_opts.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/sam_utils.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/sam_view.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/sample.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/samtools.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/stats.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/stats_isize.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/samtools/tmp_file.c.pysam.o -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -L/usr/lib64 -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/usr/lib64 -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libcsamtools.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbcftools' extension
creating /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/HMM.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/bam2bcf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/bam2bcf_indel.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
bcftools/bam2bcf_indel.c.pysam.c: In function ‘bcf_call_gap_prep’:
bcftools/bam2bcf_indel.c.pysam.c:340:37: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  340 |                     qq = (uint8_t*) calloc(qend - qbeg, 1);
      |                                     ^~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/htslib/khash.h:129,
                 from /usr/include/htslib/khash_str2int.h:28,
                 from bcftools/bam2bcf_indel.c.pysam.c:33:
/usr/include/stdlib.h:542:14: note: in a call to allocation function ‘calloc’ declared here
  542 | extern void *calloc (size_t __nmemb, size_t __size)
      |              ^~~~~~
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/bam_sample.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/bcftools.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/bin.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/ccall.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/cols.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/consensus.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/convert.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/csq.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/em.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/filter.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/gvcf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/hclust.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/kmin.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/main.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/mcall.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/mpileup.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/ploidy.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/prob1.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/regidx.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/reheader.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/smpl_ilist.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/tabix.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/tsv2vcf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/vcfannotate.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/vcfbuf.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/vcfcall.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/vcfcnv.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/vcfconcat.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/vcfconvert.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/vcffilter.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/vcfgtcheck.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/vcfindex.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/vcfisec.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/vcfmerge.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/vcfnorm.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/vcfplugin.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/vcfquery.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/vcfroh.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/vcfsom.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/vcfsort.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/vcfstats.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/vcfview.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/vcmp.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c bcftools/version.c.pysam.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c pysam/libcbcftools.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/pysam/libcbcftools.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 -Wl,--defsym=__gentoo_check_ldflags__=0 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/HMM.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/bam2bcf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/bam2bcf_indel.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/bam_sample.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/bcftools.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/bin.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/ccall.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/cols.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/consensus.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/convert.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/csq.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/em.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/filter.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/gvcf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/hclust.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/kmin.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/main.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/mcall.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/mpileup.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/ploidy.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/prob1.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/regidx.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/reheader.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/smpl_ilist.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/tabix.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/tsv2vcf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfannotate.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfbuf.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfcall.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfcnv.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfconcat.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfconvert.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcffilter.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfgtcheck.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfindex.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfisec.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfmerge.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfnorm.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfplugin.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfquery.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfroh.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfsom.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfsort.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfstats.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcfview.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/vcmp.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/bcftools/version.c.pysam.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/pysam/libcbcftools.o -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -L/usr/lib64 -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/usr/lib64 -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libcbcftools.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcutils' extension
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c pysam/libcutils.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c pysam/pysam_util.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/pysam/pysam_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 -Wl,--defsym=__gentoo_check_ldflags__=0 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/pysam/libcutils.o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/pysam/pysam_util.o -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -L/usr/lib64 -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/usr/lib64 -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcsamtools.cpython-39-x86_64-linux-gnu -lcbcftools.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libcutils.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcalignmentfile' extension
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c pysam/libcalignmentfile.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext’:
pysam/libcalignmentfile.c:30147:127: warning: passing argument 5 of ‘bam_mplp_auto’ from incompatible pointer type [-Wincompatible-pointer-types]
30147 |   __pyx_v_ret = bam_mplp_auto(__pyx_v_self->pileup_iter, (&__pyx_v_self->tid), (&__pyx_v_self->pos), (&__pyx_v_self->n_plp), (&__pyx_v_self->plp));
      |                                                                                                                              ~^~~~~~~~~~~~~~~~~~~
      |                                                                                                                               |
      |                                                                                                                               bam_pileup1_t **
In file included from pysam/htslib_util.h:4,
                 from pysam/libcalignmentfile.c:626:
/usr/include/htslib/sam.h:1709:96: note: expected ‘const bam_pileup1_t **’ but argument is of type ‘bam_pileup1_t **’
 1709 |     int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp);
      |                                                                          ~~~~~~~~~~~~~~~~~~~~~~^~~
pysam/libcalignmentfile.c: In function ‘__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext’:
pysam/libcalignmentfile.c:28085:16: warning: ignoring return value of ‘bgzf_seek’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
28085 |         (void)(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:13918:20: warning: ignoring return value of ‘sam_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
13918 |             (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr));
      |                   ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/pysam/libcalignmentfile.o -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -L/usr/lib64 -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/usr/lib64 -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libcalignmentfile.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcsamfile' extension
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c pysam/libcsamfile.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/pysam/libcsamfile.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 -Wl,--defsym=__gentoo_check_ldflags__=0 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/pysam/libcsamfile.o -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -L/usr/lib64 -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/usr/lib64 -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libcsamfile.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcalignedsegment' extension
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c pysam/libcalignedsegment.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/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_18fromstring’:
pysam/libcalignedsegment.c:14452:10: warning: ignoring return value of ‘sam_parse1’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
14452 |   (void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate));
      |         ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/pysam/libcalignedsegment.o -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -L/usr/lib64 -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/usr/lib64 -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libcalignedsegment.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libctabix' extension
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c pysam/libctabix.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/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:8794:27: warning: assignment to ‘char **’ from incompatible pointer type ‘const char **’ [-Wincompatible-pointer-types]
 8794 |         __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
      |                           ^
pysam/libctabix.c: In function ‘__pyx_pf_5pysam_9libctabix_4tabix_index’:
pysam/libctabix.c:13989:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
13989 |   __pyx_t_1 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 975, __pyx_L1_error)
      |                                       ^~~~~~~~
pysam/libctabix.c:14021:39: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
14021 |   __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 976, __pyx_L1_error)
      |                                       ^~~~~~~~
pysam/libctabix.c:14391:43: warning: overflow in conversion from ‘int’ to ‘int8_t’ {aka ‘signed char’} changes value from ‘65536’ to ‘0’ [-Woverflow]
14391 |       __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1005, __pyx_L1_error)
      |                                           ^~~~~~~~
x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/pysam/libctabix.o -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -L/usr/lib64 -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/usr/lib64 -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libctabix.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcfaidx' extension
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c pysam/libcfaidx.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/pysam/libcfaidx.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 -Wl,--defsym=__gentoo_check_ldflags__=0 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/pysam/libcfaidx.o -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -L/usr/lib64 -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/usr/lib64 -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libcfaidx.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbcf' extension
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c pysam/libcbcf.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_6close’:
pysam/libcbcf.c:66753:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
66753 |           (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
      |                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_11VariantFile_4__dealloc__’:
pysam/libcbcf.c:66478:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
66478 |           (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
      |                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function ‘__pyx_f_5pysam_7libcbcf_11VariantFile_write’:
pysam/libcbcf.c:71596:18: warning: ignoring return value of ‘bcf_hdr_write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
71596 |           (void)(bcf_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_self->header->ptr));
      |                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_22add_sample’:
pysam/libcbcf.c:35562:12: warning: ignoring return value of ‘bcf_hdr_sync’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
35562 |     (void)(bcf_hdr_sync(__pyx_v_self->ptr));
      |           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_20add_meta’:
pysam/libcbcf.c:35262:11: warning: ignoring return value of ‘bcf_hrec_add_key’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
35262 |           bcf_hrec_add_key(__pyx_v_hrec, __pyx_t_17, ((int)__pyx_t_18));
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c:35288:11: warning: ignoring return value of ‘bcf_hrec_set_val’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
35288 |           bcf_hrec_set_val(__pyx_v_hrec, (__pyx_v_hrec->nkeys - 1), __pyx_t_19, ((int)__pyx_t_18), __pyx_v_quoted);
      |           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c:35401:12: warning: ignoring return value of ‘bcf_hdr_sync’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
35401 |     (void)(bcf_hdr_sync(__pyx_v_self->ptr));
      |           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_18add_line’:
pysam/libcbcf.c:34827:12: warning: ignoring return value of ‘bcf_hdr_sync’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
34827 |     (void)(bcf_hdr_sync(__pyx_v_self->ptr));
      |           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pysam/libcbcf.c: In function ‘__pyx_pf_5pysam_7libcbcf_13VariantHeader_16add_record’:
pysam/libcbcf.c:34692:12: warning: ignoring return value of ‘bcf_hdr_sync’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
34692 |     (void)(bcf_hdr_sync(__pyx_v_self->ptr));
      |           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/pysam/libcbcf.o -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -L/usr/lib64 -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/usr/lib64 -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libcbcf.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbgzf' extension
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c pysam/libcbgzf.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/pysam/libcbgzf.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 -Wl,--defsym=__gentoo_check_ldflags__=0 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/pysam/libcbgzf.o -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -L/usr/lib64 -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/usr/lib64 -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libcbgzf.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libctabixproxies' extension
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c pysam/libctabixproxies.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/pysam/libctabixproxies.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 -Wl,--defsym=__gentoo_check_ldflags__=0 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/pysam/libctabixproxies.o -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -L/usr/lib64 -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/usr/lib64 -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libctabixproxies.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
building 'pysam.libcvcf' extension
x86_64-pc-linux-gnu-gcc -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 -fPIC -I/usr/include -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/samtools/lz4 -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/bcftools -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -I/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9 -I/usr/include/python3.9 -c pysam/libcvcf.c -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/pysam/libcvcf.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 -Wl,--defsym=__gentoo_check_ldflags__=0 -pipe -march=native -fno-diagnostics-color -O2 -falign-functions=32:25:16 /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/temp.linux-x86_64-3.9/pysam/libcvcf.o -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/pysam -L/usr/lib64 -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam -L/usr/lib64 -lz -lhts -lchtslib.cpython-39-x86_64-linux-gnu -lcutils.cpython-39-x86_64-linux-gnu -o /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libcvcf.cpython-39-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN
>>> Source compiled.
 * Skipping make test/check due to ebuild restriction.
>>> Test phase [disabled because of RESTRICT=test]: sci-biology/pysam-0.16.0.1

>>> Install sci-biology/pysam-0.16.0.1 into /var/tmp/portage/sci-biology/pysam-0.16.0.1/image
 * python3_9: running distutils-r1_run_phase distutils-r1_python_install
python3.9 setup.py install --skip-build --root=/var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is external
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
running install
running install_lib
creating /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9
creating /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr
creating /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib
creating /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9
creating /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages
creating /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libcvcf.cpython-39-x86_64-linux-gnu.so -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libctabixproxies.cpython-39-x86_64-linux-gnu.so -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libcbgzf.cpython-39-x86_64-linux-gnu.so -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libcbcf.cpython-39-x86_64-linux-gnu.so -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libcfaidx.cpython-39-x86_64-linux-gnu.so -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libctabix.cpython-39-x86_64-linux-gnu.so -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libcalignedsegment.cpython-39-x86_64-linux-gnu.so -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libcsamfile.cpython-39-x86_64-linux-gnu.so -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libcalignmentfile.cpython-39-x86_64-linux-gnu.so -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libcutils.cpython-39-x86_64-linux-gnu.so -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libcbcftools.cpython-39-x86_64-linux-gnu.so -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libcsamtools.cpython-39-x86_64-linux-gnu.so -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libchtslib.cpython-39-x86_64-linux-gnu.so -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/cbcftools_util.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/csamtools_util.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/htslib_util.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/pysam_stream.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/pysam_util.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/version.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libcalignedsegment.pxd -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libcalignmentfile.pxd -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libcbcf.pxd -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libcbcftools.pxd -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libcfaidx.pxd -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libchtslib.pxd -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libcsamfile.pxd -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libcsamtools.pxd -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libctabix.pxd -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libctabixproxies.pxd -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libcutils.pxd -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/libcvcf.pxd -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
creating /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include
creating /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools/HMM.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools/bam2bcf.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools/bam_sample.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools/bcftools.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools/bcftools.pysam.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools/bin.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools/call.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools/cols.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools/convert.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools/filter.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools/gvcf.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools/hclust.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools/hex.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools/khash_str2str.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools/kheap.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools/kmin.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools/mw.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools/ploidy.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools/prob1.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools/rbuf.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools/regidx.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools/smpl_ilist.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools/tsv2vcf.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools/variantkey.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools/vcfbuf.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools/vcmp.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/bcftools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/bcftools/config.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/bcftools
creating /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/samtools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/samtools/bam.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/samtools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/samtools/bam2bcf.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/samtools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/samtools/bam_endian.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/samtools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/samtools/bam_lpileup.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/samtools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/samtools/bam_plbuf.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/samtools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/samtools/bedidx.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/samtools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/samtools/sam.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/samtools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/samtools/sam_opts.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/samtools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/samtools/sample.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/samtools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/samtools/samtools.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/samtools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/samtools/samtools.pysam.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/samtools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/samtools/stats_isize.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/samtools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/samtools/tmp_file.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/samtools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/samtools/config.h -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/samtools
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/include/__init__.py -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/Pileup.py -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/__init__.py -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/bcftools.py -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/samtools.py -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/utils.py -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/version.py -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
copying /var/tmp/portage/sci-biology/pysam-0.16.0.1/work/pysam-0.16.0.1-python3_9/build/lib/pysam/config.py -> /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam
byte-compiling /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/include/__init__.py to __init__.cpython-39.pyc
byte-compiling /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/Pileup.py to Pileup.cpython-39.pyc
byte-compiling /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/__init__.py to __init__.cpython-39.pyc
byte-compiling /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/bcftools.py to bcftools.cpython-39.pyc
byte-compiling /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/samtools.py to samtools.cpython-39.pyc
byte-compiling /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/utils.py to utils.cpython-39.pyc
byte-compiling /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/version.py to version.cpython-39.pyc
byte-compiling /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam/config.py to config.cpython-39.pyc
writing byte-compilation script '/var/tmp/portage/sci-biology/pysam-0.16.0.1/temp/tmpm38gj8lv.py'
/usr/bin/python3.9 /var/tmp/portage/sci-biology/pysam-0.16.0.1/temp/tmpm38gj8lv.py
removing /var/tmp/portage/sci-biology/pysam-0.16.0.1/temp/tmpm38gj8lv.py
writing byte-compilation script '/var/tmp/portage/sci-biology/pysam-0.16.0.1/temp/tmp232mz61n.py'
/usr/bin/python3.9 /var/tmp/portage/sci-biology/pysam-0.16.0.1/temp/tmp232mz61n.py
removing /var/tmp/portage/sci-biology/pysam-0.16.0.1/temp/tmp232mz61n.py
running install_egg_info
running egg_info
creating pysam.egg-info
writing pysam.egg-info/PKG-INFO
writing dependency_links to pysam.egg-info/dependency_links.txt
writing top-level names to pysam.egg-info/top_level.txt
writing manifest file 'pysam.egg-info/SOURCES.txt'
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)
listing git files failed - pretending there aren't any
reading manifest file 'pysam.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'KNOWN_BUGS'
warning: no files found matching 'THANKS'
no previously-included directories found matching 'tests/'
warning: no files found matching 'samtools/configure'
warning: no files found matching 'samtools/config.mk.in'
warning: no files found matching 'samtools/config.h.in'
warning: no files found matching 'htslib/*.c'
warning: no files found matching 'htslib/*.h'
warning: no files found matching 'htslib/INSTALL'
warning: no files found matching 'htslib/NEWS'
warning: no previously-included files found matching 'htslib/config.h'
warning: no files found matching 'htslib/Makefile'
warning: no files found matching 'htslib/htslib_vars.mk'
warning: no files found matching 'htslib/configure'
warning: no files found matching 'htslib/config.mk.in'
warning: no files found matching 'htslib/config.h.in'
warning: no files found matching 'htslib/htslib.pc.in'
warning: no files found matching 'htslib/htslib/*.h'
warning: no files found matching 'htslib/cram/*.c'
warning: no files found matching 'htslib/cram/*.h'
warning: no files found matching 'htslib/os/*.c'
warning: no files found matching 'htslib/os/*.h'
adding license file 'COPYING'
adding license file 'AUTHORS'
writing manifest file 'pysam.egg-info/SOURCES.txt'
Copying pysam.egg-info to /var/tmp/portage/sci-biology/pysam-0.16.0.1/image/_python3.9/usr/lib/python3.9/site-packages/pysam-0.16.0.1-py3.9.egg-info
running install_scripts
 * Using python3.9 in global scope
 * python3_9: running distutils-r1_run_phase distutils-r1_python_install_all
>>> Completed installing sci-biology/pysam-0.16.0.1 into /var/tmp/portage/sci-biology/pysam-0.16.0.1/image

 * Final size of build directory: 62412 KiB (60.9 MiB)
 * Final size of installed tree:   6760 KiB ( 6.6 MiB)

 * Verifying compiled files in /usr/lib/python3.9/site-packages
strip: x86_64-pc-linux-gnu-strip --strip-unneeded -N __gentoo_check_ldflags__ -R .comment -R .GCC.command.line -R .note.gnu.gold-version
   /usr/lib/python3.9/site-packages/pysam/libcvcf.cpython-39-x86_64-linux-gnu.so
   /usr/lib/python3.9/site-packages/pysam/libctabixproxies.cpython-39-x86_64-linux-gnu.so
   /usr/lib/python3.9/site-packages/pysam/libcbgzf.cpython-39-x86_64-linux-gnu.so
   /usr/lib/python3.9/site-packages/pysam/libcbcf.cpython-39-x86_64-linux-gnu.so
   /usr/lib/python3.9/site-packages/pysam/libcfaidx.cpython-39-x86_64-linux-gnu.so
   /usr/lib/python3.9/site-packages/pysam/libctabix.cpython-39-x86_64-linux-gnu.so
   /usr/lib/python3.9/site-packages/pysam/libcalignedsegment.cpython-39-x86_64-linux-gnu.so
   /usr/lib/python3.9/site-packages/pysam/libcsamfile.cpython-39-x86_64-linux-gnu.so
   /usr/lib/python3.9/site-packages/pysam/libcutils.cpython-39-x86_64-linux-gnu.so
   /usr/lib/python3.9/site-packages/pysam/libcalignmentfile.cpython-39-x86_64-linux-gnu.so
   /usr/lib/python3.9/site-packages/pysam/libcsamtools.cpython-39-x86_64-linux-gnu.so
   /usr/lib/python3.9/site-packages/pysam/libcbcftools.cpython-39-x86_64-linux-gnu.so
   /usr/lib/python3.9/site-packages/pysam/libchtslib.cpython-39-x86_64-linux-gnu.so
 * checking 112 files for package collisions
>>> Merging sci-biology/pysam-0.16.0.1 to /
--- /usr/
--- /usr/lib/
--- /usr/lib/python3.9/
--- /usr/lib/python3.9/site-packages/
>>> /usr/lib/python3.9/site-packages/pysam/
>>> /usr/lib/python3.9/site-packages/pysam/libcvcf.cpython-39-x86_64-linux-gnu.so
>>> /usr/lib/python3.9/site-packages/pysam/libctabixproxies.cpython-39-x86_64-linux-gnu.so
>>> /usr/lib/python3.9/site-packages/pysam/libcbgzf.cpython-39-x86_64-linux-gnu.so
>>> /usr/lib/python3.9/site-packages/pysam/libcbcf.cpython-39-x86_64-linux-gnu.so
>>> /usr/lib/python3.9/site-packages/pysam/libcfaidx.cpython-39-x86_64-linux-gnu.so
>>> /usr/lib/python3.9/site-packages/pysam/libctabix.cpython-39-x86_64-linux-gnu.so
>>> /usr/lib/python3.9/site-packages/pysam/libcalignedsegment.cpython-39-x86_64-linux-gnu.so
>>> /usr/lib/python3.9/site-packages/pysam/libcsamfile.cpython-39-x86_64-linux-gnu.so
>>> /usr/lib/python3.9/site-packages/pysam/libcalignmentfile.cpython-39-x86_64-linux-gnu.so
>>> /usr/lib/python3.9/site-packages/pysam/libcutils.cpython-39-x86_64-linux-gnu.so
>>> /usr/lib/python3.9/site-packages/pysam/libcbcftools.cpython-39-x86_64-linux-gnu.so
>>> /usr/lib/python3.9/site-packages/pysam/libcsamtools.cpython-39-x86_64-linux-gnu.so
>>> /usr/lib/python3.9/site-packages/pysam/libchtslib.cpython-39-x86_64-linux-gnu.so
>>> /usr/lib/python3.9/site-packages/pysam/cbcftools_util.h
>>> /usr/lib/python3.9/site-packages/pysam/csamtools_util.h
>>> /usr/lib/python3.9/site-packages/pysam/htslib_util.h
>>> /usr/lib/python3.9/site-packages/pysam/pysam_stream.h
>>> /usr/lib/python3.9/site-packages/pysam/pysam_util.h
>>> /usr/lib/python3.9/site-packages/pysam/version.h
>>> /usr/lib/python3.9/site-packages/pysam/libcalignedsegment.pxd
>>> /usr/lib/python3.9/site-packages/pysam/libcalignmentfile.pxd
>>> /usr/lib/python3.9/site-packages/pysam/libcbcf.pxd
>>> /usr/lib/python3.9/site-packages/pysam/libcbcftools.pxd
>>> /usr/lib/python3.9/site-packages/pysam/libcfaidx.pxd
>>> /usr/lib/python3.9/site-packages/pysam/libchtslib.pxd
>>> /usr/lib/python3.9/site-packages/pysam/libcsamfile.pxd
>>> /usr/lib/python3.9/site-packages/pysam/libcsamtools.pxd
>>> /usr/lib/python3.9/site-packages/pysam/libctabix.pxd
>>> /usr/lib/python3.9/site-packages/pysam/libctabixproxies.pxd
>>> /usr/lib/python3.9/site-packages/pysam/libcutils.pxd
>>> /usr/lib/python3.9/site-packages/pysam/libcvcf.pxd
>>> /usr/lib/python3.9/site-packages/pysam/include/
>>> /usr/lib/python3.9/site-packages/pysam/include/bcftools/
>>> /usr/lib/python3.9/site-packages/pysam/include/bcftools/HMM.h
>>> /usr/lib/python3.9/site-packages/pysam/include/bcftools/bam2bcf.h
>>> /usr/lib/python3.9/site-packages/pysam/include/bcftools/bam_sample.h
>>> /usr/lib/python3.9/site-packages/pysam/include/bcftools/bcftools.h
>>> /usr/lib/python3.9/site-packages/pysam/include/bcftools/bcftools.pysam.h
>>> /usr/lib/python3.9/site-packages/pysam/include/bcftools/bin.h
>>> /usr/lib/python3.9/site-packages/pysam/include/bcftools/call.h
>>> /usr/lib/python3.9/site-packages/pysam/include/bcftools/cols.h
>>> /usr/lib/python3.9/site-packages/pysam/include/bcftools/convert.h
>>> /usr/lib/python3.9/site-packages/pysam/include/bcftools/filter.h
>>> /usr/lib/python3.9/site-packages/pysam/include/bcftools/gvcf.h
>>> /usr/lib/python3.9/site-packages/pysam/include/bcftools/hclust.h
>>> /usr/lib/python3.9/site-packages/pysam/include/bcftools/hex.h
>>> /usr/lib/python3.9/site-packages/pysam/include/bcftools/khash_str2str.h
>>> /usr/lib/python3.9/site-packages/pysam/include/bcftools/kheap.h
>>> /usr/lib/python3.9/site-packages/pysam/include/bcftools/kmin.h
>>> /usr/lib/python3.9/site-packages/pysam/include/bcftools/mw.h
>>> /usr/lib/python3.9/site-packages/pysam/include/bcftools/ploidy.h
>>> /usr/lib/python3.9/site-packages/pysam/include/bcftools/prob1.h
>>> /usr/lib/python3.9/site-packages/pysam/include/bcftools/rbuf.h
>>> /usr/lib/python3.9/site-packages/pysam/include/bcftools/regidx.h
>>> /usr/lib/python3.9/site-packages/pysam/include/bcftools/smpl_ilist.h
>>> /usr/lib/python3.9/site-packages/pysam/include/bcftools/tsv2vcf.h
>>> /usr/lib/python3.9/site-packages/pysam/include/bcftools/variantkey.h
>>> /usr/lib/python3.9/site-packages/pysam/include/bcftools/vcfbuf.h
>>> /usr/lib/python3.9/site-packages/pysam/include/bcftools/vcmp.h
>>> /usr/lib/python3.9/site-packages/pysam/include/bcftools/config.h
>>> /usr/lib/python3.9/site-packages/pysam/include/samtools/
>>> /usr/lib/python3.9/site-packages/pysam/include/samtools/bam.h
>>> /usr/lib/python3.9/site-packages/pysam/include/samtools/bam2bcf.h
>>> /usr/lib/python3.9/site-packages/pysam/include/samtools/bam_endian.h
>>> /usr/lib/python3.9/site-packages/pysam/include/samtools/bam_lpileup.h
>>> /usr/lib/python3.9/site-packages/pysam/include/samtools/bam_plbuf.h
>>> /usr/lib/python3.9/site-packages/pysam/include/samtools/bedidx.h
>>> /usr/lib/python3.9/site-packages/pysam/include/samtools/sam.h
>>> /usr/lib/python3.9/site-packages/pysam/include/samtools/sam_opts.h
>>> /usr/lib/python3.9/site-packages/pysam/include/samtools/sample.h
>>> /usr/lib/python3.9/site-packages/pysam/include/samtools/samtools.h
>>> /usr/lib/python3.9/site-packages/pysam/include/samtools/samtools.pysam.h
>>> /usr/lib/python3.9/site-packages/pysam/include/samtools/stats_isize.h
>>> /usr/lib/python3.9/site-packages/pysam/include/samtools/tmp_file.h
>>> /usr/lib/python3.9/site-packages/pysam/include/samtools/config.h
>>> /usr/lib/python3.9/site-packages/pysam/include/__init__.py
>>> /usr/lib/python3.9/site-packages/pysam/include/__pycache__/
>>> /usr/lib/python3.9/site-packages/pysam/include/__pycache__/__init__.cpython-39.pyc
>>> /usr/lib/python3.9/site-packages/pysam/include/__pycache__/__init__.cpython-39.opt-1.pyc
>>> /usr/lib/python3.9/site-packages/pysam/include/__pycache__/__init__.cpython-39.opt-2.pyc
>>> /usr/lib/python3.9/site-packages/pysam/Pileup.py
>>> /usr/lib/python3.9/site-packages/pysam/__init__.py
>>> /usr/lib/python3.9/site-packages/pysam/bcftools.py
>>> /usr/lib/python3.9/site-packages/pysam/samtools.py
>>> /usr/lib/python3.9/site-packages/pysam/utils.py
>>> /usr/lib/python3.9/site-packages/pysam/version.py
>>> /usr/lib/python3.9/site-packages/pysam/config.py
>>> /usr/lib/python3.9/site-packages/pysam/__pycache__/
>>> /usr/lib/python3.9/site-packages/pysam/__pycache__/Pileup.cpython-39.pyc
>>> /usr/lib/python3.9/site-packages/pysam/__pycache__/__init__.cpython-39.pyc
>>> /usr/lib/python3.9/site-packages/pysam/__pycache__/bcftools.cpython-39.pyc
>>> /usr/lib/python3.9/site-packages/pysam/__pycache__/samtools.cpython-39.pyc
>>> /usr/lib/python3.9/site-packages/pysam/__pycache__/utils.cpython-39.pyc
>>> /usr/lib/python3.9/site-packages/pysam/__pycache__/version.cpython-39.pyc
>>> /usr/lib/python3.9/site-packages/pysam/__pycache__/config.cpython-39.pyc
>>> /usr/lib/python3.9/site-packages/pysam/__pycache__/Pileup.cpython-39.opt-1.pyc
>>> /usr/lib/python3.9/site-packages/pysam/__pycache__/__init__.cpython-39.opt-1.pyc
>>> /usr/lib/python3.9/site-packages/pysam/__pycache__/bcftools.cpython-39.opt-1.pyc
>>> /usr/lib/python3.9/site-packages/pysam/__pycache__/samtools.cpython-39.opt-1.pyc
>>> /usr/lib/python3.9/site-packages/pysam/__pycache__/utils.cpython-39.opt-1.pyc
>>> /usr/lib/python3.9/site-packages/pysam/__pycache__/version.cpython-39.opt-1.pyc
>>> /usr/lib/python3.9/site-packages/pysam/__pycache__/config.cpython-39.opt-1.pyc
>>> /usr/lib/python3.9/site-packages/pysam/__pycache__/Pileup.cpython-39.opt-2.pyc
>>> /usr/lib/python3.9/site-packages/pysam/__pycache__/__init__.cpython-39.opt-2.pyc
>>> /usr/lib/python3.9/site-packages/pysam/__pycache__/bcftools.cpython-39.opt-2.pyc
>>> /usr/lib/python3.9/site-packages/pysam/__pycache__/samtools.cpython-39.opt-2.pyc
>>> /usr/lib/python3.9/site-packages/pysam/__pycache__/utils.cpython-39.opt-2.pyc
>>> /usr/lib/python3.9/site-packages/pysam/__pycache__/version.cpython-39.opt-2.pyc
>>> /usr/lib/python3.9/site-packages/pysam/__pycache__/config.cpython-39.opt-2.pyc
>>> /usr/lib/python3.9/site-packages/pysam-0.16.0.1-py3.9.egg-info/
>>> /usr/lib/python3.9/site-packages/pysam-0.16.0.1-py3.9.egg-info/SOURCES.txt
>>> /usr/lib/python3.9/site-packages/pysam-0.16.0.1-py3.9.egg-info/top_level.txt
>>> /usr/lib/python3.9/site-packages/pysam-0.16.0.1-py3.9.egg-info/dependency_links.txt
>>> /usr/lib/python3.9/site-packages/pysam-0.16.0.1-py3.9.egg-info/not-zip-safe
>>> /usr/lib/python3.9/site-packages/pysam-0.16.0.1-py3.9.egg-info/PKG-INFO
--- /usr/share/
--- /usr/share/doc/
>>> /usr/share/doc/pysam-0.16.0.1/
>>> /usr/share/doc/pysam-0.16.0.1/README.rst.bz2
>>> /usr/share/doc/pysam-0.16.0.1/AUTHORS.bz2
>>> /usr/share/doc/pysam-0.16.0.1/NEWS.bz2
>>> sci-biology/pysam-0.16.0.1 merged.
>>> Regenerating /etc/ld.so.cache...