-------------------------------------------------------------------------------
-- Phase: setup
-------------------------------------------------------------------------------

Installing /packages/All/indexinfo-0.3.1.txz
Installing /packages/All/gettext-runtime-0.21.txz
Installing /packages/All/gmake-4.3_2.txz
Installing /packages/All/libffi-3.3_1.txz
Installing /packages/All/expat-2.2.8.txz
Installing /packages/All/ncurses-6.2.20200831.txz
Installing /packages/All/readline-8.0.4.txz
Installing /packages/All/openssl-1.1.1g,1.txz
Installing /packages/All/python37-3.7.9.txz
=====
Message from python37-3.7.9:

--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:

py37-gdbm       databases/py-gdbm@py37
py37-sqlite3    databases/py-sqlite3@py37
py37-tkinter    x11-toolkits/py-tkinter@py37
Installing /packages/All/py37-setuptools-44.0.0.txz
Installing /packages/All/py37-cython-0.29.15.txz

SUCCEEDED 00:00:07

-------------------------------------------------------------------------------
-- Phase: check-sanity
-------------------------------------------------------------------------------


SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: pkg-depends
-------------------------------------------------------------------------------

===>   py37-pysam-0.16.0 depends on file: /usr/local/sbin/pkg - found

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: fetch-depends
-------------------------------------------------------------------------------


SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: fetch
-------------------------------------------------------------------------------

===>   py37-pysam-0.16.0 depends on file: /usr/local/sbin/pkg - found
===> Fetching all distfiles required by py37-pysam-0.16.0 for building

SUCCEEDED 00:00:01

-------------------------------------------------------------------------------
-- Phase: checksum
-------------------------------------------------------------------------------

===>   py37-pysam-0.16.0 depends on file: /usr/local/sbin/pkg - found
===> Fetching all distfiles required by py37-pysam-0.16.0 for building
=> SHA256 Checksum OK for pysam-0.16.0.tar.gz.

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: extract-depends
-------------------------------------------------------------------------------


SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: extract
-------------------------------------------------------------------------------

===>   py37-pysam-0.16.0 depends on file: /usr/local/sbin/pkg - found
===> Fetching all distfiles required by py37-pysam-0.16.0 for building
===>  Extracting for py37-pysam-0.16.0
=> SHA256 Checksum OK for pysam-0.16.0.tar.gz.

Extracted Memory Use:  23.46M
SUCCEEDED 00:00:01

-------------------------------------------------------------------------------
-- Phase: patch-depends
-------------------------------------------------------------------------------


SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: patch
-------------------------------------------------------------------------------

===>  Patching for py37-pysam-0.16.0
===>  Applying ports patches for py37-pysam-0.16.0 from /xports/biology/py-pysam/files

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: build-depends
-------------------------------------------------------------------------------

===>   py37-pysam-0.16.0 depends on package: gmake>=4.3 - found
===>   py37-pysam-0.16.0 depends on executable: cython-3.7 - found
===>   py37-pysam-0.16.0 depends on package: py37-setuptools>0 - found
===>   py37-pysam-0.16.0 depends on file: /usr/local/bin/python3.7 - found

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: lib-depends
-------------------------------------------------------------------------------


SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: configure
-------------------------------------------------------------------------------

===>   py37-pysam-0.16.0 depends on package: gmake>=4.3 - found
===>   py37-pysam-0.16.0 depends on executable: cython-3.7 - found
===>   py37-pysam-0.16.0 depends on package: py37-setuptools>0 - found
===>   py37-pysam-0.16.0 depends on file: /usr/local/bin/python3.7 - found
===>  Configuring for py37-pysam-0.16.0
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is shared
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
# pysam: (env) CC=cc
# pysam: (env) CFLAGS=-pipe -O2 -fno-strict-aliasing 
# pysam: (env) LDFLAGS= 
checking for gcc... cc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
checking for pkg-config... no
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking shared library type for unknown-DragonFly... plain .so
checking whether the compiler accepts -fvisibility=hidden... yes
checking how to run the C preprocessor... cpp
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking whether fdatasync is declared... no
checking for library containing log... -lm
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing recv... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... yes
checking for lzma_easy_buffer_encode in -llzma... yes
checking for libdeflate.h... no
checking for libdeflate_deflate_compress in -ldeflate... no
checking for curl_easy_pause in -lcurl... no
checking for curl_easy_init in -lcurl... no
configure: error: libcurl library not found

Support for HTTPS and other SSL-based URLs requires routines from the libcurl
library <http://curl.haxx.se/libcurl/>.  Building HTSlib with libcurl enabled
requires libcurl development files to be installed on the build machine; you
may need to ensure a package such as libcurl4-{gnutls,nss,openssl}-dev (on
Debian or Ubuntu Linux) or libcurl-devel (on RPM-based Linux distributions
or Cygwin) is installed.

Either configure with --disable-libcurl or resolve this error to build HTSlib.
checking for gcc... cc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
checking for pkg-config... no
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking shared library type for unknown-DragonFly... plain .so
checking whether the compiler accepts -fvisibility=hidden... yes
checking how to run the C preprocessor... cpp
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking whether fdatasync is declared... no
checking for library containing log... -lm
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing recv... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... yes
checking for lzma_easy_buffer_encode in -llzma... yes
checking for libdeflate.h... no
checking for libdeflate_deflate_compress in -ldeflate... no
configure: WARNING: GCS support not enabled: requires libcurl support
configure: WARNING: S3 support not enabled: requires libcurl support
checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating htslib.pc.tmp
config.status: creating config.h
# pysam: htslib configure options: --disable-libcurl
gmake[1]: ./version.sh: No such file or directory
gmake[1]: ./version.sh: No such file or directory
# pysam: htslib_config LIBHTS_OBJS=kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/string_alloc.o
# pysam: htslib_config LIBS=-llzma -lbz2 -lz -lm
# pysam: htslib_config PLATFORM=default
# pysam: config_option: ENABLE_GCS=0
# pysam: config_option: ENABLE_PLUGINS=0
# pysam: config_option: ENABLE_S3=0
# pysam: config_option: HAVE_COMMONCRYPTO=0
# pysam: config_option: HAVE_HMAC=0
# pysam: config_option: HAVE_LIBBZ2=1
# pysam: config_option: HAVE_LIBCURL=0
# pysam: config_option: HAVE_LIBDEFLATE=0
# pysam: config_option: HAVE_LIBLZMA=1
# pysam: config_option: HAVE_MMAP=1
running config

SUCCEEDED 00:00:12

-------------------------------------------------------------------------------
-- Phase: build
-------------------------------------------------------------------------------

===>  Building for py37-pysam-0.16.0
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is shared
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
# pysam: (env) CC=cc
# pysam: (env) CFLAGS=-pipe -O2 -fno-strict-aliasing 
# pysam: (env) LDFLAGS= 
checking for gcc... cc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
checking for pkg-config... no
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking shared library type for unknown-DragonFly... plain .so
checking whether the compiler accepts -fvisibility=hidden... yes
checking how to run the C preprocessor... cpp
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking whether fdatasync is declared... no
checking for library containing log... -lm
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing recv... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... yes
checking for lzma_easy_buffer_encode in -llzma... yes
checking for libdeflate.h... no
checking for libdeflate_deflate_compress in -ldeflate... no
checking for curl_easy_pause in -lcurl... no
checking for curl_easy_init in -lcurl... no
configure: error: libcurl library not found

Support for HTTPS and other SSL-based URLs requires routines from the libcurl
library <http://curl.haxx.se/libcurl/>.  Building HTSlib with libcurl enabled
requires libcurl development files to be installed on the build machine; you
may need to ensure a package such as libcurl4-{gnutls,nss,openssl}-dev (on
Debian or Ubuntu Linux) or libcurl-devel (on RPM-based Linux distributions
or Cygwin) is installed.

Either configure with --disable-libcurl or resolve this error to build HTSlib.
checking for gcc... cc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
checking for pkg-config... no
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking shared library type for unknown-DragonFly... plain .so
checking whether the compiler accepts -fvisibility=hidden... yes
checking how to run the C preprocessor... cpp
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking whether fdatasync is declared... no
checking for library containing log... -lm
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing recv... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... yes
checking for lzma_easy_buffer_encode in -llzma... yes
checking for libdeflate.h... no
checking for libdeflate_deflate_compress in -ldeflate... no
configure: WARNING: GCS support not enabled: requires libcurl support
configure: WARNING: S3 support not enabled: requires libcurl support
checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating htslib.pc.tmp
config.status: creating config.h
config.status: config.h is unchanged
# pysam: htslib configure options: --disable-libcurl
gmake[1]: ./version.sh: No such file or directory
gmake[1]: ./version.sh: No such file or directory
# pysam: htslib_config LIBHTS_OBJS=kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/string_alloc.o
# pysam: htslib_config LIBS=-llzma -lbz2 -lz -lm
# pysam: htslib_config PLATFORM=default
# pysam: config_option: ENABLE_GCS=0
# pysam: config_option: ENABLE_PLUGINS=0
# pysam: config_option: ENABLE_S3=0
# pysam: config_option: HAVE_COMMONCRYPTO=0
# pysam: config_option: HAVE_HMAC=0
# pysam: config_option: HAVE_LIBBZ2=1
# pysam: config_option: HAVE_LIBCURL=0
# pysam: config_option: HAVE_LIBDEFLATE=0
# pysam: config_option: HAVE_LIBLZMA=1
# pysam: config_option: HAVE_MMAP=1
running build
running build_py
creating build
creating build/lib.dragonfly-5.9-x86_64-3.7
creating build/lib.dragonfly-5.9-x86_64-3.7/pysam
copying pysam/config.py -> build/lib.dragonfly-5.9-x86_64-3.7/pysam
copying pysam/bcftools.py -> build/lib.dragonfly-5.9-x86_64-3.7/pysam
copying pysam/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/pysam
copying pysam/Pileup.py -> build/lib.dragonfly-5.9-x86_64-3.7/pysam
copying pysam/utils.py -> build/lib.dragonfly-5.9-x86_64-3.7/pysam
copying pysam/samtools.py -> build/lib.dragonfly-5.9-x86_64-3.7/pysam
copying pysam/version.py -> build/lib.dragonfly-5.9-x86_64-3.7/pysam
creating build/lib.dragonfly-5.9-x86_64-3.7/pysam/include
copying pysam/include/__init__.py -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
package init file 'htslib/__init__.py' not found (or not a regular file)
package init file 'htslib/htslib/__init__.py' not found (or not a regular file)
copying pysam/libcvcf.pxd -> build/lib.dragonfly-5.9-x86_64-3.7/pysam
copying pysam/libchtslib.pxd -> build/lib.dragonfly-5.9-x86_64-3.7/pysam
copying pysam/libcbcftools.pxd -> build/lib.dragonfly-5.9-x86_64-3.7/pysam
copying pysam/libctabixproxies.pxd -> build/lib.dragonfly-5.9-x86_64-3.7/pysam
copying pysam/libctabix.pxd -> build/lib.dragonfly-5.9-x86_64-3.7/pysam
copying pysam/libcsamtools.pxd -> build/lib.dragonfly-5.9-x86_64-3.7/pysam
copying pysam/libcalignedsegment.pxd -> build/lib.dragonfly-5.9-x86_64-3.7/pysam
copying pysam/libcbcf.pxd -> build/lib.dragonfly-5.9-x86_64-3.7/pysam
copying pysam/libcalignmentfile.pxd -> build/lib.dragonfly-5.9-x86_64-3.7/pysam
copying pysam/libcfaidx.pxd -> build/lib.dragonfly-5.9-x86_64-3.7/pysam
copying pysam/libcutils.pxd -> build/lib.dragonfly-5.9-x86_64-3.7/pysam
copying pysam/libcsamfile.pxd -> build/lib.dragonfly-5.9-x86_64-3.7/pysam
copying pysam/htslib_util.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam
copying pysam/csamtools_util.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam
copying pysam/cbcftools_util.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam
copying pysam/version.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam
copying pysam/pysam_util.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam
copying pysam/pysam_stream.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam
creating build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/samtools
copying samtools/bam2bcf.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/samtools
copying samtools/tmp_file.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/samtools
copying samtools/bam_lpileup.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/samtools
copying samtools/sample.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/samtools
copying samtools/samtools.pysam.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/samtools
copying samtools/samtools.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/samtools
copying samtools/bam_plbuf.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/samtools
copying samtools/bedidx.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/samtools
copying samtools/bam.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/samtools
copying samtools/bam_endian.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/samtools
copying samtools/stats_isize.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/samtools
copying samtools/sam_opts.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/samtools
copying samtools/sam.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/samtools
copying samtools/config.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/samtools
creating build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools
copying bcftools/bam_sample.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools
copying bcftools/bcftools.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools
copying bcftools/convert.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools
copying bcftools/kmin.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools
copying bcftools/filter.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools
copying bcftools/ploidy.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools
copying bcftools/mw.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools
copying bcftools/hclust.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools
copying bcftools/rbuf.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools
copying bcftools/bin.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools
copying bcftools/kheap.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools
copying bcftools/variantkey.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools
copying bcftools/cols.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools
copying bcftools/HMM.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools
copying bcftools/call.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools
copying bcftools/khash_str2str.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools
copying bcftools/gvcf.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools
copying bcftools/tsv2vcf.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools
copying bcftools/bam2bcf.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools
copying bcftools/vcfbuf.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools
copying bcftools/prob1.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools
copying bcftools/hex.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools
copying bcftools/regidx.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools
copying bcftools/smpl_ilist.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools
copying bcftools/bcftools.pysam.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools
copying bcftools/vcmp.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools
copying bcftools/config.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools
creating build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib
copying htslib/config.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib
copying htslib/thread_pool_internal.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib
copying htslib/hfile_internal.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib
copying htslib/bcf_sr_sort.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib
copying htslib/hts_internal.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib
copying htslib/sam_internal.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib
copying htslib/textutils_internal.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib
copying htslib/header.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib
creating build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib
copying htslib/htslib/thread_pool.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib
copying htslib/htslib/bgzf.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib
copying htslib/htslib/kbitset.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib
copying htslib/htslib/hts.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib
copying htslib/htslib/regidx.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib
copying htslib/htslib/hts_os.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib
copying htslib/htslib/kfunc.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib
copying htslib/htslib/kseq.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib
copying htslib/htslib/kstring.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib
copying htslib/htslib/knetfile.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib
copying htslib/htslib/hts_defs.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib
copying htslib/htslib/khash.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib
copying htslib/htslib/klist.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib
copying htslib/htslib/sam.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib
copying htslib/htslib/faidx.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib
copying htslib/htslib/tbx.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib
copying htslib/htslib/hfile.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib
copying htslib/htslib/cram.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib
copying htslib/htslib/synced_bcf_reader.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib
copying htslib/htslib/ksort.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib
copying htslib/htslib/vcf.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib
copying htslib/htslib/hts_endian.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib
copying htslib/htslib/vcf_sweep.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib
copying htslib/htslib/khash_str2int.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib
copying htslib/htslib/hts_log.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib
copying htslib/htslib/vcfutils.h -> build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib
Fixing build/lib.dragonfly-5.9-x86_64-3.7/pysam/config.py build/lib.dragonfly-5.9-x86_64-3.7/pysam/bcftools.py build/lib.dragonfly-5.9-x86_64-3.7/pysam/__init__.py build/lib.dragonfly-5.9-x86_64-3.7/pysam/Pileup.py build/lib.dragonfly-5.9-x86_64-3.7/pysam/utils.py build/lib.dragonfly-5.9-x86_64-3.7/pysam/samtools.py build/lib.dragonfly-5.9-x86_64-3.7/pysam/version.py build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/__init__.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
Fixing build/lib.dragonfly-5.9-x86_64-3.7/pysam/config.py build/lib.dragonfly-5.9-x86_64-3.7/pysam/bcftools.py build/lib.dragonfly-5.9-x86_64-3.7/pysam/__init__.py build/lib.dragonfly-5.9-x86_64-3.7/pysam/Pileup.py build/lib.dragonfly-5.9-x86_64-3.7/pysam/utils.py build/lib.dragonfly-5.9-x86_64-3.7/pysam/samtools.py build/lib.dragonfly-5.9-x86_64-3.7/pysam/version.py build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/__init__.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
running build_ext
skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
skipping 'pysam/libcsamtools.c' Cython extension (up-to-date)
skipping 'pysam/libcbcftools.c' Cython extension (up-to-date)
skipping 'pysam/libcutils.c' Cython extension (up-to-date)
skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date)
skipping 'pysam/libcsamfile.c' Cython extension (up-to-date)
skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date)
skipping 'pysam/libctabix.c' Cython extension (up-to-date)
skipping 'pysam/libcfaidx.c' Cython extension (up-to-date)
skipping 'pysam/libcbcf.c' Cython extension (up-to-date)
skipping 'pysam/libcbgzf.c' Cython extension (up-to-date)
skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date)
skipping 'pysam/libcvcf.c' Cython extension (up-to-date)
building 'pysam.libchtslib' extension
creating build/temp.dragonfly-5.9-x86_64-3.7
creating build/temp.dragonfly-5.9-x86_64-3.7/pysam
creating build/temp.dragonfly-5.9-x86_64-3.7/htslib
creating build/temp.dragonfly-5.9-x86_64-3.7/htslib/cram
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c pysam/libchtslib.c -o build/temp.dragonfly-5.9-x86_64-3.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c pysam/htslib_util.c -o build/temp.dragonfly-5.9-x86_64-3.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/kfunc.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/kfunc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/knetfile.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/knetfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/kstring.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/kstring.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/bcf_sr_sort.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/bcf_sr_sort.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/bgzf.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/bgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/errmod.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/errmod.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/faidx.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/faidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/header.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/header.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/hfile.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/hfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/hfile_net.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/hfile_net.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/hts.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/hts.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/hts_os.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/hts_os.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/md5.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/md5.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/multipart.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/multipart.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/probaln.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/probaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/realn.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/realn.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/regidx.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/regidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/region.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/region.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/sam.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/sam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/synced_bcf_reader.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/synced_bcf_reader.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/vcf_sweep.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/vcf_sweep.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/tbx.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/tbx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/textutils.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/textutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/thread_pool.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/thread_pool.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/vcf.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/vcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/vcfutils.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/vcfutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/cram/cram_codecs.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/cram/cram_codecs.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/cram/cram_decode.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/cram/cram_decode.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/cram/cram_encode.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/cram/cram_encode.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/cram/cram_external.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/cram/cram_external.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/cram/cram_index.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/cram/cram_index.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/cram/cram_io.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/cram/cram_io.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/cram/cram_samtools.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/cram/cram_samtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/cram/cram_stats.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/cram/cram_stats.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/cram/mFILE.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/cram/mFILE.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/cram/open_trace_file.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/cram/open_trace_file.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/cram/pooled_alloc.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/cram/pooled_alloc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/cram/rANS_static.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/cram/rANS_static.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c htslib/cram/string_alloc.c -o build/temp.dragonfly-5.9-x86_64-3.7/htslib/cram/string_alloc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/pysam/libchtslib.o build/temp.dragonfly-5.9-x86_64-3.7/pysam/htslib_util.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/kfunc.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/knetfile.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/kstring.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/bcf_sr_sort.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/bgzf.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/errmod.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/faidx.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/header.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/hfile.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/hfile_net.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/hts.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/hts_os.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/md5.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/multipart.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/probaln.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/realn.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/regidx.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/region.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/sam.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/synced_bcf_reader.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/vcf_sweep.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/tbx.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/textutils.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/thread_pool.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/vcf.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/vcfutils.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/cram/cram_codecs.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/cram/cram_decode.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/cram/cram_encode.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/cram/cram_external.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/cram/cram_index.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/cram/cram_io.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/cram/cram_samtools.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/cram/cram_stats.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/cram/mFILE.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/cram/open_trace_file.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/cram/pooled_alloc.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/cram/rANS_static.o build/temp.dragonfly-5.9-x86_64-3.7/htslib/cram/string_alloc.o -L/construction/biology/py-pysam/pysam-0.16.0/pysam -L/construction/biology/py-pysam/pysam-0.16.0/pysam -L/construction/biology/py-pysam/pysam-0.16.0 -L/construction/biology/py-pysam/pysam-0.16.0/build/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/pysam/libchtslib.so -Wl,-rpath,$ORIGIN
building 'pysam.libcsamtools' extension
creating build/temp.dragonfly-5.9-x86_64-3.7/samtools
creating build/temp.dragonfly-5.9-x86_64-3.7/samtools/lz4
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c pysam/libcsamtools.c -o build/temp.dragonfly-5.9-x86_64-3.7/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/bam_reheader.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/bam_plcmd.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/bam_sort.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/coverage.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/sam.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/bam_color.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/bam_addrprg.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/bam_split.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/bam_aux.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/bam_lpileup.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/cut_target.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/sample.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/bamshuf.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/faidx.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/dict.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/sam_utils.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/bedidx.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/bam_mate.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/bam_stat.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/bedcov.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/bam.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/bam2bcf.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/padding.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/bam_markdup.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/bam_flags.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/bam_md.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/bam2depth.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/bam_fastq.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_fastq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/bam_index.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/bam_rmdup.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/bam_plbuf.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/bam_rmdupse.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/phase.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/bam_quickcheck.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/stats_isize.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/sam_opts.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/samtools.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/bamtk.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/tmp_file.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/stats.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/sam_view.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/bam_cat.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c samtools/lz4/lz4.c -o build/temp.dragonfly-5.9-x86_64-3.7/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/pysam/libcsamtools.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_reheader.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_plcmd.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_sort.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/coverage.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/sam.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_color.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_addrprg.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam2bcf_indel.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_split.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_aux.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_lpileup.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/cut_target.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/sample.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bamshuf.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/faidx.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/dict.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/sam_utils.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bedidx.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_mate.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_stat.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bedcov.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam2bcf.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/padding.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_markdup.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_flags.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_md.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam2depth.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_fastq.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_index.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_rmdup.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_plbuf.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_rmdupse.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/phase.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_quickcheck.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/stats_isize.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/sam_opts.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/samtools.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bamtk.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/tmp_file.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/stats.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/sam_view.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/bam_cat.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/samtools/lz4/lz4.o -L/construction/biology/py-pysam/pysam-0.16.0/pysam -L/construction/biology/py-pysam/pysam-0.16.0/pysam -L/construction/biology/py-pysam/pysam-0.16.0 -L/construction/biology/py-pysam/pysam-0.16.0/build/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/pysam/libcsamtools.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbcftools' extension
creating build/temp.dragonfly-5.9-x86_64-3.7/bcftools
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c pysam/libcbcftools.c -o build/temp.dragonfly-5.9-x86_64-3.7/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/mpileup.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/csq.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/vcfannotate.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/regidx.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/hclust.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/vcfcnv.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/filter.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/ccall.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/bin.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/HMM.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/main.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/vcfconvert.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/vcfmerge.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/vcfbuf.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/mcall.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/bcftools.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/kmin.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/bam_sample.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/bam2bcf.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/vcfindex.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/vcfisec.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/em.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/vcfconcat.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/consensus.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/tsv2vcf.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/reheader.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/cols.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/convert.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/gvcf.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/prob1.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/vcfcall.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
In function 'init_data',
    inlined from 'main_vcfcall' at bcftools/vcfcall.c.pysam.c:1062:5:
bcftools/vcfcall.c.pysam.c:655:39: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
         args->aux.ploidy = (uint8_t*) malloc(args->nsamples);
                                       ^~~~~~~~~~~~~~~~~~~~~~
In file included from /construction/biology/py-pysam/pysam-0.16.0/htslib/htslib/kstring.h:30,
                 from /construction/biology/py-pysam/pysam-0.16.0/htslib/htslib/vcf.h:41,
                 from bcftools/vcfcall.c.pysam.c:34:
bcftools/vcfcall.c.pysam.c: In function 'main_vcfcall':
/usr/include/stdlib.h:105:7: note: in a call to allocation function 'malloc' declared here
 void *malloc(size_t) __malloclike __heedresult __alloc_size(1);
       ^~~~~~
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/tabix.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/smpl_ilist.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/ploidy.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/vcffilter.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/vcfstats.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/vcfroh.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/vcfsort.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/vcfsom.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/vcfnorm.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/vcfquery.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/vcfplugin.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/vcfview.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/version.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c bcftools/vcmp.c.pysam.c -o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/pysam/libcbcftools.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/mpileup.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/csq.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfannotate.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/regidx.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/hclust.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfcnv.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/filter.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/ccall.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/bin.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfgtcheck.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/bam2bcf_indel.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/HMM.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/main.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfconvert.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfmerge.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfbuf.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/mcall.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/bcftools.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/kmin.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/bam_sample.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/bam2bcf.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfindex.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfisec.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/em.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfconcat.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/consensus.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/tsv2vcf.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/reheader.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/cols.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/convert.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/gvcf.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/prob1.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfcall.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/tabix.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/smpl_ilist.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/ploidy.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcffilter.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfstats.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfroh.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfsort.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfsom.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfnorm.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfquery.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfplugin.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcfview.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/version.c.pysam.o build/temp.dragonfly-5.9-x86_64-3.7/bcftools/vcmp.c.pysam.o -L/construction/biology/py-pysam/pysam-0.16.0/pysam -L/construction/biology/py-pysam/pysam-0.16.0/pysam -L/construction/biology/py-pysam/pysam-0.16.0 -L/construction/biology/py-pysam/pysam-0.16.0/build/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/pysam/libcbcftools.so -Wl,-rpath,$ORIGIN
building 'pysam.libcutils' extension
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c pysam/libcutils.c -o build/temp.dragonfly-5.9-x86_64-3.7/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c pysam/pysam_util.c -o build/temp.dragonfly-5.9-x86_64-3.7/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/pysam/libcutils.o build/temp.dragonfly-5.9-x86_64-3.7/pysam/pysam_util.o -L/construction/biology/py-pysam/pysam-0.16.0/pysam -L/construction/biology/py-pysam/pysam-0.16.0/pysam -L/construction/biology/py-pysam/pysam-0.16.0 -L/construction/biology/py-pysam/pysam-0.16.0/build/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lcsamtools -lcbcftools -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/pysam/libcutils.so -Wl,-rpath,$ORIGIN
building 'pysam.libcalignmentfile' extension
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c pysam/libcalignmentfile.c -o build/temp.dragonfly-5.9-x86_64-3.7/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:30101:127: warning: passing argument 5 of 'bam_mplp_auto' from incompatible pointer type [-Wincompatible-pointer-types]
   __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));
                                                                                                                              ~^~~~~~~~~~~~~~~~~~~
In file included from pysam/htslib_util.h:4,
                 from pysam/libcalignmentfile.c:605:
/construction/biology/py-pysam/pysam-0.16.0/htslib/htslib/sam.h:1709:96: note: expected 'const bam_pileup1_t **' {aka 'const struct <anonymous> **'} but argument is of type 'bam_pileup1_t **' {aka 'struct <anonymous> **'}
     int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp);
                                                                          ~~~~~~~~~~~~~~~~~~~~~~^~~
cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/pysam/libcalignmentfile.o -L/construction/biology/py-pysam/pysam-0.16.0/pysam -L/construction/biology/py-pysam/pysam-0.16.0/pysam -L/construction/biology/py-pysam/pysam-0.16.0 -L/construction/biology/py-pysam/pysam-0.16.0/build/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lcutils -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/pysam/libcalignmentfile.so -Wl,-rpath,$ORIGIN
building 'pysam.libcsamfile' extension
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c pysam/libcsamfile.c -o build/temp.dragonfly-5.9-x86_64-3.7/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/pysam/libcsamfile.o -L/construction/biology/py-pysam/pysam-0.16.0/pysam -L/construction/biology/py-pysam/pysam-0.16.0/pysam -L/construction/biology/py-pysam/pysam-0.16.0 -L/construction/biology/py-pysam/pysam-0.16.0/build/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lcutils -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/pysam/libcsamfile.so -Wl,-rpath,$ORIGIN
building 'pysam.libcalignedsegment' extension
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c pysam/libcalignedsegment.c -o build/temp.dragonfly-5.9-x86_64-3.7/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/pysam/libcalignedsegment.o -L/construction/biology/py-pysam/pysam-0.16.0/pysam -L/construction/biology/py-pysam/pysam-0.16.0/pysam -L/construction/biology/py-pysam/pysam-0.16.0 -L/construction/biology/py-pysam/pysam-0.16.0/build/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lcutils -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/pysam/libcalignedsegment.so -Wl,-rpath,$ORIGIN
building 'pysam.libctabix' extension
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c pysam/libctabix.c -o build/temp.dragonfly-5.9-x86_64-3.7/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
pysam/libctabix.c: In function '__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__':
pysam/libctabix.c:8752:27: warning: assignment to 'char **' from incompatible pointer type 'const char **' [-Wincompatible-pointer-types]
         __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
                           ^
In file included from pysam/libctabix.c:612:
pysam/libctabix.c: In function '__pyx_pf_5pysam_9libctabix_4tabix_index':
/construction/biology/py-pysam/pysam-0.16.0/htslib/htslib/tbx.h:41:21: warning: overflow in conversion from 'int' to 'int8_t' {aka 'signed char'} changes value from '65536' to '0' [-Woverflow]
 #define TBX_UCSC    0x10000
                     ^~~~~~~
pysam/libctabix.c:13947:39: note: in expansion of macro 'TBX_UCSC'
   __pyx_t_1 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 975, __pyx_L1_error)
                                       ^~~~~~~~
/construction/biology/py-pysam/pysam-0.16.0/htslib/htslib/tbx.h:41:21: warning: overflow in conversion from 'int' to 'int8_t' {aka 'signed char'} changes value from '65536' to '0' [-Woverflow]
 #define TBX_UCSC    0x10000
                     ^~~~~~~
pysam/libctabix.c:13979:39: note: in expansion of macro 'TBX_UCSC'
   __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 976, __pyx_L1_error)
                                       ^~~~~~~~
/construction/biology/py-pysam/pysam-0.16.0/htslib/htslib/tbx.h:41:21: warning: overflow in conversion from 'int' to 'int8_t' {aka 'signed char'} changes value from '65536' to '0' [-Woverflow]
 #define TBX_UCSC    0x10000
                     ^~~~~~~
pysam/libctabix.c:14349:43: note: in expansion of macro 'TBX_UCSC'
       __pyx_t_3 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_3)) __PYX_ERR(0, 1005, __pyx_L1_error)
                                           ^~~~~~~~
cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/pysam/libctabix.o -L/construction/biology/py-pysam/pysam-0.16.0/pysam -L/construction/biology/py-pysam/pysam-0.16.0/pysam -L/construction/biology/py-pysam/pysam-0.16.0 -L/construction/biology/py-pysam/pysam-0.16.0/build/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lcutils -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/pysam/libctabix.so -Wl,-rpath,$ORIGIN
building 'pysam.libcfaidx' extension
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c pysam/libcfaidx.c -o build/temp.dragonfly-5.9-x86_64-3.7/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/pysam/libcfaidx.o -L/construction/biology/py-pysam/pysam-0.16.0/pysam -L/construction/biology/py-pysam/pysam-0.16.0/pysam -L/construction/biology/py-pysam/pysam-0.16.0 -L/construction/biology/py-pysam/pysam-0.16.0/build/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lcutils -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/pysam/libcfaidx.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbcf' extension
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c pysam/libcbcf.c -o build/temp.dragonfly-5.9-x86_64-3.7/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/pysam/libcbcf.o -L/construction/biology/py-pysam/pysam-0.16.0/pysam -L/construction/biology/py-pysam/pysam-0.16.0/pysam -L/construction/biology/py-pysam/pysam-0.16.0 -L/construction/biology/py-pysam/pysam-0.16.0/build/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lcutils -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/pysam/libcbcf.so -Wl,-rpath,$ORIGIN
building 'pysam.libcbgzf' extension
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c pysam/libcbgzf.c -o build/temp.dragonfly-5.9-x86_64-3.7/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/pysam/libcbgzf.o -L/construction/biology/py-pysam/pysam-0.16.0/pysam -L/construction/biology/py-pysam/pysam-0.16.0/pysam -L/construction/biology/py-pysam/pysam-0.16.0 -L/construction/biology/py-pysam/pysam-0.16.0/build/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lcutils -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/pysam/libcbgzf.so -Wl,-rpath,$ORIGIN
building 'pysam.libctabixproxies' extension
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c pysam/libctabixproxies.c -o build/temp.dragonfly-5.9-x86_64-3.7/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/pysam/libctabixproxies.o -L/construction/biology/py-pysam/pysam-0.16.0/pysam -L/construction/biology/py-pysam/pysam-0.16.0/pysam -L/construction/biology/py-pysam/pysam-0.16.0 -L/construction/biology/py-pysam/pysam-0.16.0/build/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lcutils -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/pysam/libctabixproxies.so -Wl,-rpath,$ORIGIN
building 'pysam.libcvcf' extension
cc -Wno-unused-result -Wsign-compare -DNDEBUG -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -fPIC -I/construction/biology/py-pysam/pysam-0.16.0/htslib -I/construction/biology/py-pysam/pysam-0.16.0/samtools -I/construction/biology/py-pysam/pysam-0.16.0/samtools/lz4 -I/construction/biology/py-pysam/pysam-0.16.0/bcftools -I/construction/biology/py-pysam/pysam-0.16.0/pysam -I/construction/biology/py-pysam/pysam-0.16.0 -I/usr/local/include/python3.7m -c pysam/libcvcf.c -o build/temp.dragonfly-5.9-x86_64-3.7/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -pipe -O2 -fno-strict-aliasing build/temp.dragonfly-5.9-x86_64-3.7/pysam/libcvcf.o -L/construction/biology/py-pysam/pysam-0.16.0/pysam -L/construction/biology/py-pysam/pysam-0.16.0/pysam -L/construction/biology/py-pysam/pysam-0.16.0 -L/construction/biology/py-pysam/pysam-0.16.0/build/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -Lbuild/lib.dragonfly-5.9-x86_64-3.7/pysam -L/usr/local/lib -lz -llzma -lbz2 -lz -lm -lchtslib -lcutils -lpython3.7m -o build/lib.dragonfly-5.9-x86_64-3.7/pysam/libcvcf.so -Wl,-rpath,$ORIGIN

SUCCEEDED 00:04:54

-------------------------------------------------------------------------------
-- Phase: run-depends
-------------------------------------------------------------------------------

===>   py37-pysam-0.16.0 depends on executable: cython-3.7 - found
===>   py37-pysam-0.16.0 depends on package: py37-setuptools>0 - found
===>   py37-pysam-0.16.0 depends on file: /usr/local/bin/python3.7 - found

SUCCEEDED 00:00:00

-------------------------------------------------------------------------------
-- Phase: stage
-------------------------------------------------------------------------------

===>  Staging for py37-pysam-0.16.0
===>   py37-pysam-0.16.0 depends on executable: cython-3.7 - found
===>   py37-pysam-0.16.0 depends on package: py37-setuptools>0 - found
===>   py37-pysam-0.16.0 depends on file: /usr/local/bin/python3.7 - found
===>   Generating temporary packing list
# pysam: cython is available - using cythonize if necessary
# pysam: htslib mode is shared
# pysam: HTSLIB_CONFIGURE_OPTIONS=None
# pysam: (env) CC=cc
# pysam: (env) CFLAGS=-pipe -O2 -fno-strict-aliasing 
# pysam: (env) LDFLAGS= 
checking for gcc... cc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
checking for pkg-config... no
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking shared library type for unknown-DragonFly... plain .so
checking whether the compiler accepts -fvisibility=hidden... yes
checking how to run the C preprocessor... cpp
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking whether fdatasync is declared... no
checking for library containing log... -lm
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing recv... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... yes
checking for lzma_easy_buffer_encode in -llzma... yes
checking for libdeflate.h... no
checking for libdeflate_deflate_compress in -ldeflate... no
checking for curl_easy_pause in -lcurl... no
checking for curl_easy_init in -lcurl... no
configure: error: libcurl library not found

Support for HTTPS and other SSL-based URLs requires routines from the libcurl
library <http://curl.haxx.se/libcurl/>.  Building HTSlib with libcurl enabled
requires libcurl development files to be installed on the build machine; you
may need to ensure a package such as libcurl4-{gnutls,nss,openssl}-dev (on
Debian or Ubuntu Linux) or libcurl-devel (on RPM-based Linux distributions
or Cygwin) is installed.

Either configure with --disable-libcurl or resolve this error to build HTSlib.
checking for gcc... cc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
checking for pkg-config... no
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking shared library type for unknown-DragonFly... plain .so
checking whether the compiler accepts -fvisibility=hidden... yes
checking how to run the C preprocessor... cpp
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking whether fdatasync is declared... no
checking for library containing log... -lm
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing recv... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... yes
checking for lzma_easy_buffer_encode in -llzma... yes
checking for libdeflate.h... no
checking for libdeflate_deflate_compress in -ldeflate... no
configure: WARNING: GCS support not enabled: requires libcurl support
configure: WARNING: S3 support not enabled: requires libcurl support
checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating htslib.pc.tmp
config.status: creating config.h
config.status: config.h is unchanged
# pysam: htslib configure options: --disable-libcurl
gmake[1]: ./version.sh: No such file or directory
gmake[1]: ./version.sh: No such file or directory
# pysam: htslib_config LIBHTS_OBJS=kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/string_alloc.o
# pysam: htslib_config LIBS=-llzma -lbz2 -lz -lm
# pysam: htslib_config PLATFORM=default
# pysam: config_option: ENABLE_GCS=0
# pysam: config_option: ENABLE_PLUGINS=0
# pysam: config_option: ENABLE_S3=0
# pysam: config_option: HAVE_COMMONCRYPTO=0
# pysam: config_option: HAVE_HMAC=0
# pysam: config_option: HAVE_LIBBZ2=1
# pysam: config_option: HAVE_LIBCURL=0
# pysam: config_option: HAVE_LIBDEFLATE=0
# pysam: config_option: HAVE_LIBLZMA=1
# pysam: config_option: HAVE_MMAP=1
running install
running build
running build_py
copying pysam/config.py -> build/lib.dragonfly-5.9-x86_64-3.7/pysam
package init file 'samtools/__init__.py' not found (or not a regular file)
package init file 'bcftools/__init__.py' not found (or not a regular file)
package init file 'htslib/__init__.py' not found (or not a regular file)
package init file 'htslib/htslib/__init__.py' not found (or not a regular file)
Fixing build/lib.dragonfly-5.9-x86_64-3.7/pysam/config.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
Fixing build/lib.dragonfly-5.9-x86_64-3.7/pysam/config.py
Skipping optional fixer: buffer
Skipping optional fixer: idioms
Skipping optional fixer: set_literal
Skipping optional fixer: ws_comma
running build_ext
skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
skipping 'pysam/libcsamtools.c' Cython extension (up-to-date)
skipping 'pysam/libcbcftools.c' Cython extension (up-to-date)
skipping 'pysam/libcutils.c' Cython extension (up-to-date)
skipping 'pysam/libcalignmentfile.c' Cython extension (up-to-date)
skipping 'pysam/libcsamfile.c' Cython extension (up-to-date)
skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date)
skipping 'pysam/libctabix.c' Cython extension (up-to-date)
skipping 'pysam/libcfaidx.c' Cython extension (up-to-date)
skipping 'pysam/libcbcf.c' Cython extension (up-to-date)
skipping 'pysam/libcbgzf.c' Cython extension (up-to-date)
skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date)
skipping 'pysam/libcvcf.c' Cython extension (up-to-date)
running install_lib
creating /construction/biology/py-pysam/stage/usr/local/lib/python3.7
creating /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages
creating /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/Pileup.py -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/libcbcf.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/libcsamfile.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/config.py -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/libcalignmentfile.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/libcbcftools.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/samtools.py -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
creating /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include
creating /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib
creating /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib/klist.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib/kseq.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib/tbx.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib/knetfile.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib/vcf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib/hts.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib/hts_log.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib/regidx.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib/ksort.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib/kstring.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib/khash_str2int.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib/kbitset.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib/vcf_sweep.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib/khash.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib/bgzf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib/hts_os.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib/kfunc.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib/sam.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib/hfile.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib/vcfutils.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib/hts_endian.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib/hts_defs.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib/cram.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib/faidx.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib/synced_bcf_reader.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/htslib/thread_pool.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/header.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/thread_pool_internal.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/hfile_internal.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/config.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/textutils_internal.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/hts_internal.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/bcf_sr_sort.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/htslib/sam_internal.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/htslib
creating /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools/hex.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools/mw.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools/rbuf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools/cols.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools/vcmp.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools/hclust.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools/kmin.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools/bam2bcf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools/vcfbuf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools/bcftools.pysam.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools/tsv2vcf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools/call.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools/prob1.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools/smpl_ilist.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools/kheap.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools/regidx.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools/convert.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools/khash_str2str.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools/variantkey.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools/bin.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools/config.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools/bam_sample.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools/filter.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools/bcftools.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools/gvcf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools/HMM.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/bcftools/ploidy.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/bcftools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/__init__.py -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include
creating /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/samtools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/samtools/bam.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/samtools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/samtools/bam2bcf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/samtools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/samtools/config.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/samtools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/samtools/samtools.pysam.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/samtools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/samtools/bedidx.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/samtools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/samtools/tmp_file.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/samtools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/samtools/stats_isize.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/samtools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/samtools/sam.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/samtools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/samtools/sample.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/samtools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/samtools/sam_opts.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/samtools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/samtools/bam_endian.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/samtools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/samtools/bam_plbuf.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/samtools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/samtools/bam_lpileup.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/samtools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/include/samtools/samtools.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/samtools
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/libctabix.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/libcutils.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/libcbcf.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/libctabix.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/libcvcf.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/libchtslib.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/htslib_util.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/cbcftools_util.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/libctabixproxies.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/libcfaidx.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/csamtools_util.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/libcbcftools.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/libcsamtools.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/version.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/pysam_util.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/libcalignedsegment.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/libcsamfile.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/libcalignmentfile.pxd -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/pysam_stream.h -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/libcutils.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/libctabixproxies.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/libcalignedsegment.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/libcvcf.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/libcsamtools.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/utils.py -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/bcftools.py -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/libcbgzf.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/libcfaidx.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/__init__.py -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/libchtslib.so -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
copying build/lib.dragonfly-5.9-x86_64-3.7/pysam/version.py -> /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam
byte-compiling /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/Pileup.py to Pileup.cpython-37.pyc
byte-compiling /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/config.py to config.cpython-37.pyc
byte-compiling /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/samtools.py to samtools.cpython-37.pyc
byte-compiling /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/include/__init__.py to __init__.cpython-37.pyc
byte-compiling /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/utils.py to utils.cpython-37.pyc
byte-compiling /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/bcftools.py to bcftools.cpython-37.pyc
byte-compiling /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/__init__.py to __init__.cpython-37.pyc
byte-compiling /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam/version.py to version.cpython-37.pyc
writing byte-compilation script '/tmp/tmpanhtlxu7.py'
/usr/local/bin/python3.7 /tmp/tmpanhtlxu7.py
removing /tmp/tmpanhtlxu7.py
running install_egg_info
running 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
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/INSTALL'
warning: no files found matching 'htslib/NEWS'
writing manifest file 'pysam.egg-info/SOURCES.txt'
Copying pysam.egg-info to /construction/biology/py-pysam/stage/usr/local/lib/python3.7/site-packages/pysam-0.16.0-py3.7.egg-info
running install_scripts
writing list of installed files to '/construction/biology/py-pysam/.PLIST.pymodtmp'
====> Compressing man pages (compress-man)
====> Running Q/A tests (stage-qa)
Warning: 'lib/python3.7/site-packages/pysam/libcutils.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD}
Warning: 'lib/python3.7/site-packages/pysam/libcbcftools.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD}
Warning: 'lib/python3.7/site-packages/pysam/libcsamtools.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD}
Warning: 'lib/python3.7/site-packages/pysam/libcbgzf.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD}
Warning: 'lib/python3.7/site-packages/pysam/libcvcf.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD}
Warning: 'lib/python3.7/site-packages/pysam/libctabixproxies.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD}
Warning: 'lib/python3.7/site-packages/pysam/libctabix.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD}
Warning: 'lib/python3.7/site-packages/pysam/libcalignmentfile.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD}
Warning: 'lib/python3.7/site-packages/pysam/libcbcf.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD}
Warning: 'lib/python3.7/site-packages/pysam/libcalignedsegment.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD}
Warning: 'lib/python3.7/site-packages/pysam/libcsamfile.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD}
Warning: 'lib/python3.7/site-packages/pysam/libchtslib.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD}
Warning: 'lib/python3.7/site-packages/pysam/libcfaidx.so' is not stripped consider trying INSTALL_TARGET=install-strip or using ${STRIP_CMD}
Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks

SUCCEEDED 00:00:11

-------------------------------------------------------------------------------
-- Phase: check-plist
-------------------------------------------------------------------------------

====> Checking for pkg-plist issues (check-plist)
===> Parsing plist
===> Checking for items in STAGEDIR missing from pkg-plist
===> Checking for items in pkg-plist which are not in STAGEDIR
===> No pkg-plist issues found (check-plist)

SUCCEEDED 00:00:01

-------------------------------------------------------------------------------
-- Phase: package
-------------------------------------------------------------------------------

===>  Building package for py37-pysam-0.16.0
file sizes/checksums   [135]:   0%
file sizes/checksums   [135]:  74%
file sizes/checksums   [135]: 100%
packing files          [135]:   0%
packing files          [135]:  74%
packing files          [135]: 100%
packing directories      [0]:   0%
packing directories      [0]: 100%

SUCCEEDED 00:00:06
TOTAL TIME 00:05:34