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py-pysam: Remove obsolete log
Module Name: pkgsrc-wip
Committed By: Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By: outpaddling
Date: Mon Nov 5 22:56:43 2018 -0600
Changeset: bbefca8aa4fb05f7c5295f7499e92f3c4b312e56
Removed Files:
py-pysam/log
Log Message:
py-pysam: Remove obsolete log
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=bbefca8aa4fb05f7c5295f7499e92f3c4b312e56
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
py-pysam/log | 908 -----------------------------------------------------------
1 file changed, 908 deletions(-)
diffs:
diff --git a/py-pysam/log b/py-pysam/log
deleted file mode 100644
index 6380c72c50..0000000000
--- a/py-pysam/log
+++ /dev/null
@@ -1,908 +0,0 @@
-Remove distfile? y/[n] ===> Cleaning for py27-pysam-0.15.1
-WARN: log: Unexpected file found.
-0 errors and 1 warning found.
-Press return to continue...===> Deinstalling for py27-pysam-0.15.1
-=> Bootstrap dependency digest>=20010302: found digest-20180917
-===> Checking for vulnerabilities in py27-pysam-0.15.1
-=> Checksum SHA1 OK for pysam-0.15.1.tar.gz
-=> Checksum RMD160 OK for pysam-0.15.1.tar.gz
-=> Checksum SHA512 OK for pysam-0.15.1.tar.gz
-===> Installing dependencies for py27-pysam-0.15.1
-==========================================================================
-The following variables will affect the build process of this package,
-py27-pysam-0.15.1. Their current value is shown below:
-
- * PYTHON_VERSION_DEFAULT = 27
- * SSLBASE (defined)
- * SSLCERTS = /usr/pkg/etc/openssl/certs
- * SSLDIR = /usr/pkg/etc/openssl
- * SSLKEYS = /usr/pkg/etc/openssl/private
-
-Based on these variables, the following variables have been set:
-
- * PYPACKAGE = python27
-
-You may want to abort the process now with CTRL-C and change their value
-before continuing. Be sure to run `/usr/pkg/bin/bmake.bin clean' after
-the changes.
-==========================================================================
-=> Tool dependency nbpatch-[0-9]*: found nbpatch-20151107
-=> Tool dependency checkperms>=1.1: found checkperms-1.12
-=> Build dependency gcc6>=6.1: found gcc6-6.4.0nb4
-=> Build dependency cwrappers>=20150314: found cwrappers-20180325
-=> Full dependency py27-setuptools>=0.8: found py27-setuptools-40.4.3
-=> Full dependency python27>=2.7.1nb2: found python27-2.7.15nb1
-=> Full dependency ncurses>=6.0: found ncurses-6.1nb2
-=> Full dependency py27-cython>=0.12.1: found py27-cython-0.28.5
-=> Full dependency curl>=7.61.0nb2: found curl-7.61.1
-=> Full dependency zlib>=1.2.3: found zlib-1.2.11
-=> Full dependency bzip2>=1.0.3: found bzip2-1.0.6nb1
-=> Full dependency xz>=5.0.0: found xz-5.2.4
-===> Overriding tools for py27-pysam-0.15.1
-===> Extracting for py27-pysam-0.15.1
-===> Patching for py27-pysam-0.15.1
-=> Applying pkgsrc patches for py27-pysam-0.15.1
-=> Verifying /usr/pkgsrc/wip/py-pysam/patches/patch-setup.py
-=> Applying pkgsrc patch /usr/pkgsrc/wip/py-pysam/patches/patch-setup.py
-Hmm... Looks like a unified diff to me...
-The text leading up to this was:
---------------------------
-|$NetBSD$
-|
-|# Portability
-|
-|--- setup.py.orig 2017-04-19 05:48:10 UTC
-|+++ setup.py
---------------------------
-Patching file setup.py using Plan A...
-Hunk #1 succeeded at 66 (offset 6 lines).
-done
-===> Creating toolchain wrappers for py27-pysam-0.15.1
-===> Configuring for py27-pysam-0.15.1
-=> Checking for portability problems in extracted files
-===> Building for py27-pysam-0.15.1
-(cd /usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/ && /usr/bin/env USETOOLS=no PTHREAD_CFLAGS=\ -pthread\ PTHREAD_LDFLAGS=\ -pthread PTHREAD_LIBS=-lpthread\ -lrt PTHREADBASE=/usr DL_CFLAGS= DL_LDFLAGS= DL_LIBS= PYTHON=/usr/pkg/bin/python2.7 CC=cc CFLAGS=-O2\ -D_FORTIFY_SOURCE=2\ -I/usr/include\ -I/usr/pkg/include\ -I/usr/pkg/include/ncurses CPPFLAGS=-I/usr/include\ -I/usr/pkg/include\ -I/usr/pkg/include/ncurses CXX=c++ CXXFLAGS=-O2\ -D_FORTIFY_SOURCE=2\ -I/usr/include\ -I/usr/pkg/include\ -I/usr/pkg/include/ncurses COMPILER_RPATH_FLAG=-Wl,-R F77=gfortran FC=gfortran FFLAGS=-O LANG=C LC_ALL=C LC_COLLATE=C LC_CTYPE=C LC_MESSAGES=C LC_MONETARY=C LC_NUMERIC=C LC_TIME=C LDFLAGS=-L/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so\ -Wl,-R/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so\ -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0\ -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0\ -L/usr/pkg/gcc6/lib64\ -Wl,-R/usr/pkg/gcc6/lib64\ -L/usr/lib64\ -Wl,-R/usr/lib64\
-L/usr/pkg/lib\ -Wl,-R/usr/pkg/lib LINKER_RPATH_FLAG=-R PATH=/usr/pkgsrc/wip/py-pysam/work/.cwrapper/bin:/usr/pkgsrc/wip/py-pysam/work/.buildlink/bin:/usr/pkgsrc/wip/py-pysam/work/.gcc/bin:/usr/pkgsrc/wip/py-pysam/work/.tools/bin:/usr/pkg/bin:/home/bacon/scripts:/usr/pkg/bin:/usr/local/bin:/home/bacon/scripts:/home/bacon/miniconda3/bin:/usr/pkg/bin:/usr/pkg/sbin:/usr/pkg/gcc5/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/bacon/.local/bin:/home/bacon/bin:/sbin:/usr/sbin:/usr/local/sbin:/usr/pkg/bin:/usr/pkg/bin PREFIX=/usr/pkg MAKELEVEL=0 CONFIG_SITE= PKG_SYSCONFDIR=/usr/pkg/etc CXXCPP=cpp HOME=/usr/pkgsrc/wip/py-pysam/work/.home CWRAPPERS_CONFIG_DIR=/usr/pkgsrc/wip/py-pysam/work/.cwrapper/config CPP=cpp LOCALBASE=/usr/pkg X11BASE=/usr/pkg PKGMANDIR=man PKGINFODIR=info PKGGNUDIR=gnu/ MAKECONF=/dev/null OBJECT_FMT=ELF USETOOLS=no BSD_INSTALL_PROGRAM=/bin/install\ -c\ -s\ -o\ root\ -g\ root\ -m\ 755 BSD_INSTALL_SCRIPT=/bin/install\ -c\ -o\ root\ -g\ root\ -m\ 755 BSD_INST
ALL_LIB=/bin/install\ -c\ -o\ root\ -g\ root\ -m\ 755 BSD_INSTALL_DATA=/bin/install\ -c\ -o\ root\ -g\ root\ -m\ 644 BSD_INSTALL_MAN=/bin/install\ -c\ -o\ root\ -g\ root\ -m\ 644 BSD_INSTALL=/bin/install BSD_INSTALL_PROGRAM_DIR=/bin/install\ -d\ -o\ root\ -g\ root\ -m\ 755 BSD_INSTALL_SCRIPT_DIR=/bin/install\ -d\ -o\ root\ -g\ root\ -m\ 755 BSD_INSTALL_LIB_DIR=/bin/install\ -d\ -o\ root\ -g\ root\ -m\ 755 BSD_INSTALL_DATA_DIR=/bin/install\ -d\ -o\ root\ -g\ root\ -m\ 755 BSD_INSTALL_MAN_DIR=/bin/install\ -d\ -o\ root\ -g\ root\ -m\ 755 BSD_INSTALL_GAME=/bin/install\ -c\ -s\ -o\ root\ -g\ root\ -m\ 2555 BSD_INSTALL_GAME_DATA=/bin/install\ -c\ -o\ root\ -g\ root\ -m\ 664 BSD_INSTALL_GAME_DIR=/bin/install\ -d\ -o\ root\ -g\ root\ -m\ 775 INSTALL_INFO= MAKEINFO=/usr/pkgsrc/wip/py-pysam/work/.tools/bin/makeinfo FLEX= BISON= PKG_CONFIG= PKG_CONFIG_LIBDIR=/usr/pkgsrc/wip/py-pysam/work/.buildlink/lib64/pkgconfig:/usr/pkgsrc/wip/py-pysam/work/.buildlink/lib/pkgconfig:/usr/pkgsrc/wip/py-pysam
/work/.buildlink/share/pkgconfig PKG_CONFIG_LOG=/usr/pkgsrc/wip/py-pysam/work/.pkg-config.log PKG_CONFIG_PATH= CWRAPPERS_CONFIG_DIR=/usr/pkgsrc/wip/py-pysam/work/.cwrapper/config /usr/pkg/bin/python2.7 setup.py build )
-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/pkgsrc/wip/py-pysam/work/.tools/bin/grep
-checking for C compiler warning flags... -Wall
-checking for special C compiler options needed for large files... no
-checking for _FILE_OFFSET_BITS value needed for large files... no
-checking for _LARGEFILE_SOURCE value needed for large files... no
-checking shared library type for unknown-Linux... plain .so
-checking how to run the C preprocessor... cpp
-checking for egrep... /usr/pkgsrc/wip/py-pysam/work/.tools/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... yes
-checking for fdatasync... yes
-checking for library containing log... -lm
-checking for zlib.h... yes
-checking for inflate in -lz... yes
-checking for library containing 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... yes
-checking for CCHmac... no
-checking for library containing HMAC... -lcrypto
-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
-gmake: ./version.sh: Command not found
-gmake: ./version.sh: Command not found
-# pysam: cython is available - using cythonize if necessary
-# pysam: htslib mode is shared
-# pysam: HTSLIB_CONFIGURE_OPTIONS=None
-# pysam: htslib configure options: --enable-libcurl
-# pysam: htslib_config LIBS=-llzma -lbz2 -lz -lm -lcurl -lcrypto
-# pysam: htslib_config PLATFORM=default
-# pysam: htslib_config LIBHTS_OBJS=kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o hfile_libcurl.o hfile_gcs.o hfile_s3.o
-# pysam: htslib_config LDFLAGS=-L/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -Wl,-R/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib
-# pysam: config_option: ENABLE_PLUGINS=0
-# pysam: config_option: HAVE_COMMONCRYPTO=0
-# pysam: config_option: HAVE_GMTIME_R=1
-# pysam: config_option: HAVE_HMAC=1
-# pysam: config_option: HAVE_IRODS=0
-# pysam: config_option: HAVE_LIBCURL=1
-# pysam: config_option: HAVE_MMAP=1
-running build
-running build_py
-creating build
-creating build/lib.linux-x86_64-2.7
-creating build/lib.linux-x86_64-2.7/pysam
-copying pysam/Pileup.py -> build/lib.linux-x86_64-2.7/pysam
-copying pysam/__init__.py -> build/lib.linux-x86_64-2.7/pysam
-copying pysam/bcftools.py -> build/lib.linux-x86_64-2.7/pysam
-copying pysam/config.py -> build/lib.linux-x86_64-2.7/pysam
-copying pysam/samtools.py -> build/lib.linux-x86_64-2.7/pysam
-copying pysam/utils.py -> build/lib.linux-x86_64-2.7/pysam
-copying pysam/version.py -> build/lib.linux-x86_64-2.7/pysam
-creating build/lib.linux-x86_64-2.7/pysam/include
-copying pysam/include/__init__.py -> build/lib.linux-x86_64-2.7/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 'samtools/win32/__init__.py' not found (or not a regular file)
-package init file 'htslib/__init__.py' not found (or not a regular file)
-package init file 'htslib/htslib/__init__.py' not found (or not a regular file)
-copying pysam/libcalignedsegment.pxd -> build/lib.linux-x86_64-2.7/pysam
-copying pysam/libcalignmentfile.pxd -> build/lib.linux-x86_64-2.7/pysam
-copying pysam/libcbcf.pxd -> build/lib.linux-x86_64-2.7/pysam
-copying pysam/libcbcftools.pxd -> build/lib.linux-x86_64-2.7/pysam
-copying pysam/libcfaidx.pxd -> build/lib.linux-x86_64-2.7/pysam
-copying pysam/libchtslib.pxd -> build/lib.linux-x86_64-2.7/pysam
-copying pysam/libcsamfile.pxd -> build/lib.linux-x86_64-2.7/pysam
-copying pysam/libcsamtools.pxd -> build/lib.linux-x86_64-2.7/pysam
-copying pysam/libctabix.pxd -> build/lib.linux-x86_64-2.7/pysam
-copying pysam/libctabixproxies.pxd -> build/lib.linux-x86_64-2.7/pysam
-copying pysam/libcutils.pxd -> build/lib.linux-x86_64-2.7/pysam
-copying pysam/libcvcf.pxd -> build/lib.linux-x86_64-2.7/pysam
-copying pysam/cbcftools_util.h -> build/lib.linux-x86_64-2.7/pysam
-copying pysam/csamtools_util.h -> build/lib.linux-x86_64-2.7/pysam
-copying pysam/htslib_util.h -> build/lib.linux-x86_64-2.7/pysam
-copying pysam/pysam_stream.h -> build/lib.linux-x86_64-2.7/pysam
-copying pysam/pysam_util.h -> build/lib.linux-x86_64-2.7/pysam
-creating build/lib.linux-x86_64-2.7/pysam/include/samtools
-copying samtools/bam.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
-copying samtools/bam2bcf.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
-copying samtools/bam_endian.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
-copying samtools/bam_lpileup.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
-copying samtools/bam_plbuf.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
-copying samtools/bedidx.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
-copying samtools/sam.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
-copying samtools/sam_header.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
-copying samtools/sam_opts.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
-copying samtools/sample.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
-copying samtools/samtools.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
-copying samtools/samtools.pysam.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
-copying samtools/stats_isize.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
-copying samtools/tmp_file.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
-copying samtools/version.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
-copying samtools/config.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools
-creating build/lib.linux-x86_64-2.7/pysam/include/bcftools
-copying bcftools/HMM.h -> build/lib.linux-x86_64-2.7/pysam/include/bcftools
-copying bcftools/bam2bcf.h -> build/lib.linux-x86_64-2.7/pysam/include/bcftools
-copying bcftools/bam_sample.h -> build/lib.linux-x86_64-2.7/pysam/include/bcftools
-copying bcftools/bcftools.h -> build/lib.linux-x86_64-2.7/pysam/include/bcftools
-copying bcftools/bcftools.pysam.h -> build/lib.linux-x86_64-2.7/pysam/include/bcftools
-copying bcftools/bin.h -> build/lib.linux-x86_64-2.7/pysam/include/bcftools
-copying bcftools/call.h -> build/lib.linux-x86_64-2.7/pysam/include/bcftools
-copying bcftools/convert.h -> build/lib.linux-x86_64-2.7/pysam/include/bcftools
-copying bcftools/filter.h -> build/lib.linux-x86_64-2.7/pysam/include/bcftools
-copying bcftools/gvcf.h -> build/lib.linux-x86_64-2.7/pysam/include/bcftools
-copying bcftools/hclust.h -> build/lib.linux-x86_64-2.7/pysam/include/bcftools
-copying bcftools/khash_str2str.h -> build/lib.linux-x86_64-2.7/pysam/include/bcftools
-copying bcftools/kheap.h -> build/lib.linux-x86_64-2.7/pysam/include/bcftools
-copying bcftools/kmin.h -> build/lib.linux-x86_64-2.7/pysam/include/bcftools
-copying bcftools/mw.h -> build/lib.linux-x86_64-2.7/pysam/include/bcftools
-copying bcftools/ploidy.h -> build/lib.linux-x86_64-2.7/pysam/include/bcftools
-copying bcftools/prob1.h -> build/lib.linux-x86_64-2.7/pysam/include/bcftools
-copying bcftools/rbuf.h -> build/lib.linux-x86_64-2.7/pysam/include/bcftools
-copying bcftools/regidx.h -> build/lib.linux-x86_64-2.7/pysam/include/bcftools
-copying bcftools/smpl_ilist.h -> build/lib.linux-x86_64-2.7/pysam/include/bcftools
-copying bcftools/tsv2vcf.h -> build/lib.linux-x86_64-2.7/pysam/include/bcftools
-copying bcftools/vcfbuf.h -> build/lib.linux-x86_64-2.7/pysam/include/bcftools
-copying bcftools/vcmp.h -> build/lib.linux-x86_64-2.7/pysam/include/bcftools
-copying bcftools/version.h -> build/lib.linux-x86_64-2.7/pysam/include/bcftools
-copying bcftools/config.h -> build/lib.linux-x86_64-2.7/pysam/include/bcftools
-creating build/lib.linux-x86_64-2.7/pysam/include/samtools/win32
-copying samtools/win32/xcurses.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools/win32
-copying samtools/win32/zconf.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools/win32
-copying samtools/win32/zlib.h -> build/lib.linux-x86_64-2.7/pysam/include/samtools/win32
-creating build/lib.linux-x86_64-2.7/pysam/include/htslib
-copying htslib/bcf_sr_sort.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib
-copying htslib/hfile_internal.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib
-copying htslib/hts_internal.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib
-copying htslib/textutils_internal.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib
-copying htslib/thread_pool_internal.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib
-copying htslib/version.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib
-copying htslib/config.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib
-creating build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib
-copying htslib/htslib/bgzf.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib
-copying htslib/htslib/cram.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib
-copying htslib/htslib/faidx.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib
-copying htslib/htslib/hfile.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib
-copying htslib/htslib/hts.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib
-copying htslib/htslib/hts_defs.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib
-copying htslib/htslib/hts_endian.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib
-copying htslib/htslib/hts_log.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib
-copying htslib/htslib/hts_os.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib
-copying htslib/htslib/kbitset.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib
-copying htslib/htslib/kfunc.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib
-copying htslib/htslib/khash.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib
-copying htslib/htslib/khash_str2int.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib
-copying htslib/htslib/klist.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib
-copying htslib/htslib/knetfile.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib
-copying htslib/htslib/kseq.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib
-copying htslib/htslib/ksort.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib
-copying htslib/htslib/kstring.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib
-copying htslib/htslib/regidx.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib
-copying htslib/htslib/sam.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib
-copying htslib/htslib/synced_bcf_reader.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib
-copying htslib/htslib/tbx.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib
-copying htslib/htslib/thread_pool.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib
-copying htslib/htslib/vcf.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib
-copying htslib/htslib/vcf_sweep.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib
-copying htslib/htslib/vcfutils.h -> build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib
-running build_ext
-skipping 'pysam/libchtslib.c' Cython extension (up-to-date)
-building 'pysam.libchtslib' extension
-creating build/temp.linux-x86_64-2.7
-creating build/temp.linux-x86_64-2.7/pysam
-creating build/temp.linux-x86_64-2.7/htslib
-creating build/temp.linux-x86_64-2.7/htslib/cram
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c pysam/libchtslib.c -o build/temp.linux-x86_64-2.7/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c pysam/htslib_util.c -o build/temp.linux-x86_64-2.7/pysam/htslib_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/kfunc.c -o build/temp.linux-x86_64-2.7/htslib/kfunc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/knetfile.c -o build/temp.linux-x86_64-2.7/htslib/knetfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/kstring.c -o build/temp.linux-x86_64-2.7/htslib/kstring.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/bcf_sr_sort.c -o build/temp.linux-x86_64-2.7/htslib/bcf_sr_sort.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/bgzf.c -o build/temp.linux-x86_64-2.7/htslib/bgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/errmod.c -o build/temp.linux-x86_64-2.7/htslib/errmod.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/faidx.c -o build/temp.linux-x86_64-2.7/htslib/faidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/hfile.c -o build/temp.linux-x86_64-2.7/htslib/hfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/hfile_net.c -o build/temp.linux-x86_64-2.7/htslib/hfile_net.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/hts.c -o build/temp.linux-x86_64-2.7/htslib/hts.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/hts_os.c -o build/temp.linux-x86_64-2.7/htslib/hts_os.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/md5.c -o build/temp.linux-x86_64-2.7/htslib/md5.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/multipart.c -o build/temp.linux-x86_64-2.7/htslib/multipart.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/probaln.c -o build/temp.linux-x86_64-2.7/htslib/probaln.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/realn.c -o build/temp.linux-x86_64-2.7/htslib/realn.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/regidx.c -o build/temp.linux-x86_64-2.7/htslib/regidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/sam.c -o build/temp.linux-x86_64-2.7/htslib/sam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/synced_bcf_reader.c -o build/temp.linux-x86_64-2.7/htslib/synced_bcf_reader.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/vcf_sweep.c -o build/temp.linux-x86_64-2.7/htslib/vcf_sweep.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/tbx.c -o build/temp.linux-x86_64-2.7/htslib/tbx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/textutils.c -o build/temp.linux-x86_64-2.7/htslib/textutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/thread_pool.c -o build/temp.linux-x86_64-2.7/htslib/thread_pool.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/vcf.c -o build/temp.linux-x86_64-2.7/htslib/vcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/vcfutils.c -o build/temp.linux-x86_64-2.7/htslib/vcfutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/cram/cram_codecs.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_codecs.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/cram/cram_decode.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_decode.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/cram/cram_encode.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_encode.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/cram/cram_external.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_external.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/cram/cram_index.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_index.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/cram/cram_io.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_io.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/cram/cram_samtools.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_samtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/cram/cram_stats.c -o build/temp.linux-x86_64-2.7/htslib/cram/cram_stats.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/cram/files.c -o build/temp.linux-x86_64-2.7/htslib/cram/files.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/cram/mFILE.c -o build/temp.linux-x86_64-2.7/htslib/cram/mFILE.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/cram/open_trace_file.c -o build/temp.linux-x86_64-2.7/htslib/cram/open_trace_file.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/cram/pooled_alloc.c -o build/temp.linux-x86_64-2.7/htslib/cram/pooled_alloc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/cram/rANS_static.c -o build/temp.linux-x86_64-2.7/htslib/cram/rANS_static.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/cram/sam_header.c -o build/temp.linux-x86_64-2.7/htslib/cram/sam_header.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/cram/string_alloc.c -o build/temp.linux-x86_64-2.7/htslib/cram/string_alloc.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/hfile_libcurl.c -o build/temp.linux-x86_64-2.7/htslib/hfile_libcurl.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/hfile_gcs.c -o build/temp.linux-x86_64-2.7/htslib/hfile_gcs.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c htslib/hfile_s3.c -o build/temp.linux-x86_64-2.7/htslib/hfile_s3.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -shared -L/tmp/pkgbuild/lang/python27/work/Python-2.7.15 -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -pthread -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -Wl,-R/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses build/temp.linux-x86_64-2.7/pysam/libchtslib.o build/temp.linux-x86_64-2.7/pysam/htslib_util.o build/temp.linux-x86_64-2.7/htslib/kfunc.o build/temp.linux-x86_64-2.7/htslib/knetfile.o build/temp.linux-x86_64-2.7/htslib/kst
ring.o build/temp.linux-x86_64-2.7/htslib/bcf_sr_sort.o build/temp.linux-x86_64-2.7/htslib/bgzf.o build/temp.linux-x86_64-2.7/htslib/errmod.o build/temp.linux-x86_64-2.7/htslib/faidx.o build/temp.linux-x86_64-2.7/htslib/hfile.o build/temp.linux-x86_64-2.7/htslib/hfile_net.o build/temp.linux-x86_64-2.7/htslib/hts.o build/temp.linux-x86_64-2.7/htslib/hts_os.o build/temp.linux-x86_64-2.7/htslib/md5.o build/temp.linux-x86_64-2.7/htslib/multipart.o build/temp.linux-x86_64-2.7/htslib/probaln.o build/temp.linux-x86_64-2.7/htslib/realn.o build/temp.linux-x86_64-2.7/htslib/regidx.o build/temp.linux-x86_64-2.7/htslib/sam.o build/temp.linux-x86_64-2.7/htslib/synced_bcf_reader.o build/temp.linux-x86_64-2.7/htslib/vcf_sweep.o build/temp.linux-x86_64-2.7/htslib/tbx.o build/temp.linux-x86_64-2.7/htslib/textutils.o build/temp.linux-x86_64-2.7/htslib/thread_pool.o build/temp.linux-x86_64-2.7/htslib/vcf.o build/temp.linux-x86_64-2.7/htslib/vcfutils.o build/temp.linux-x86_64-2.7/htslib/cram/cram_codecs
.o build/temp.linux-x86_64-2.7/htslib/cram/cram_decode.o build/temp.linux-x86_64-2.7/htslib/cram/cram_encode.o build/temp.linux-x86_64-2.7/htslib/cram/cram_external.o build/temp.linux-x86_64-2.7/htslib/cram/cram_index.o build/temp.linux-x86_64-2.7/htslib/cram/cram_io.o build/temp.linux-x86_64-2.7/htslib/cram/cram_samtools.o build/temp.linux-x86_64-2.7/htslib/cram/cram_stats.o build/temp.linux-x86_64-2.7/htslib/cram/files.o build/temp.linux-x86_64-2.7/htslib/cram/mFILE.o build/temp.linux-x86_64-2.7/htslib/cram/open_trace_file.o build/temp.linux-x86_64-2.7/htslib/cram/pooled_alloc.o build/temp.linux-x86_64-2.7/htslib/cram/rANS_static.o build/temp.linux-x86_64-2.7/htslib/cram/sam_header.o build/temp.linux-x86_64-2.7/htslib/cram/string_alloc.o build/temp.linux-x86_64-2.7/htslib/hfile_libcurl.o build/temp.linux-x86_64-2.7/htslib/hfile_gcs.o build/temp.linux-x86_64-2.7/htslib/hfile_s3.o -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -
L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/build/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -L/usr/pkg/lib -lz -llzma -lbz2 -lz -lm -lcurl -lcrypto -lpython2.7 -o build/lib.linux-x86_64-2.7/pysam/libchtslib.so -Wl,-rpath,$ORIGIN -L/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -Wl,-R/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib
-skipping 'pysam/libcsamtools.c' Cython extension (up-to-date)
-building 'pysam.libcsamtools' extension
-creating build/temp.linux-x86_64-2.7/samtools
-creating build/temp.linux-x86_64-2.7/samtools/lz4
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c pysam/libcsamtools.c -o build/temp.linux-x86_64-2.7/pysam/libcsamtools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/bam.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/bam2bcf.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/bam2depth.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam2depth.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/bam_addrprg.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_addrprg.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/bam_aux.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_aux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/bam_cat.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_cat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/bam_color.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_color.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/bam_flags.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_flags.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/bam_import.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_import.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/bam_index.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_index.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/bam_lpileup.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_lpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/bam_markdup.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_markdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/bam_mate.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_mate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/bam_md.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_md.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/bam_plbuf.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_plbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/bam_plcmd.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_plcmd.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/bam_quickcheck.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_quickcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/bam_reheader.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/bam_rmdup.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_rmdup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_rmdupse.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/bam_sort.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_sort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/bam_split.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_split.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/bam_stat.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/bamshuf.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/bamtk.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/bedcov.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/bedidx.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/cut_target.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/dict.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/faidx.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/padding.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/phase.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/sam.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/sam.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/sam_header.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/sam_header.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/sam_opts.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/sam_utils.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/sam_view.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/sample.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/samtools.pysam.c -o build/temp.linux-x86_64-2.7/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/stats.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/stats_isize.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/tmp_file.c.pysam.c -o build/temp.linux-x86_64-2.7/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c samtools/lz4/lz4.c -o build/temp.linux-x86_64-2.7/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -shared -L/tmp/pkgbuild/lang/python27/work/Python-2.7.15 -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -pthread -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -Wl,-R/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses build/temp.linux-x86_64-2.7/pysam/libcsamtools.o build/temp.linux-x86_64-2.7/samtools/bam.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam2bcf.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam2bcf_indel.c.pysam.o build/
temp.linux-x86_64-2.7/samtools/bam2depth.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_addrprg.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_aux.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_cat.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_color.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_flags.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_import.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_index.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_lpileup.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_markdup.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_mate.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_md.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_plbuf.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_plcmd.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_quickcheck.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_reheader.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_rmdup.c.pysam.o build/temp.linux-x86_64-2.7/
samtools/bam_rmdupse.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_sort.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_split.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bam_stat.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bamshuf.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bamtk.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bedcov.c.pysam.o build/temp.linux-x86_64-2.7/samtools/bedidx.c.pysam.o build/temp.linux-x86_64-2.7/samtools/cut_target.c.pysam.o build/temp.linux-x86_64-2.7/samtools/dict.c.pysam.o build/temp.linux-x86_64-2.7/samtools/faidx.c.pysam.o build/temp.linux-x86_64-2.7/samtools/padding.c.pysam.o build/temp.linux-x86_64-2.7/samtools/phase.c.pysam.o build/temp.linux-x86_64-2.7/samtools/sam.c.pysam.o build/temp.linux-x86_64-2.7/samtools/sam_header.c.pysam.o build/temp.linux-x86_64-2.7/samtools/sam_opts.c.pysam.o build/temp.linux-x86_64-2.7/samtools/sam_utils.c.pysam.o build/temp.linux-x86_64-2.7/samtools/sam_view.c.pysam.o build/temp.linux-x86_64-2.7/samt
ools/sample.c.pysam.o build/temp.linux-x86_64-2.7/samtools/samtools.pysam.o build/temp.linux-x86_64-2.7/samtools/stats.c.pysam.o build/temp.linux-x86_64-2.7/samtools/stats_isize.c.pysam.o build/temp.linux-x86_64-2.7/samtools/tmp_file.c.pysam.o build/temp.linux-x86_64-2.7/samtools/lz4/lz4.o -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/build/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -L/usr/pkg/lib -lz -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib -lpython2.7 -o build/lib.linux-x86_64-2.7/pysam/libcsamtools.so -Wl,-rpath,$ORIGIN -L/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -Wl,-R/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/g
cc6/lib64 -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib
-skipping 'pysam/libcbcftools.c' Cython extension (up-to-date)
-building 'pysam.libcbcftools' extension
-creating build/temp.linux-x86_64-2.7/bcftools
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c pysam/libcbcftools.c -o build/temp.linux-x86_64-2.7/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/HMM.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/bam2bcf.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/bam_sample.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/bcftools.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/bin.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/ccall.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/consensus.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/convert.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/csq.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/em.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/filter.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/gvcf.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/hclust.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/kmin.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/main.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/mcall.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/mpileup.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/ploidy.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/prob1.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/regidx.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/reheader.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/tabix.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/vcfannotate.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/vcfbuf.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/vcfcall.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/vcfcnv.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/vcfconcat.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/vcfconvert.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/vcffilter.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/vcfindex.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/vcfisec.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/vcfmerge.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/vcfnorm.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/vcfplugin.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/vcfquery.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/vcfroh.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/vcfsom.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/vcfsort.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/vcfstats.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/vcfview.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/vcmp.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c bcftools/version.c.pysam.c -o build/temp.linux-x86_64-2.7/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -shared -L/tmp/pkgbuild/lang/python27/work/Python-2.7.15 -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -pthread -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -Wl,-R/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses build/temp.linux-x86_64-2.7/pysam/libcbcftools.o build/temp.linux-x86_64-2.7/bcftools/HMM.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/bam2bcf.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/bam2bcf_indel.c.pysam.o build/
temp.linux-x86_64-2.7/bcftools/bam_sample.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/bcftools.pysam.o build/temp.linux-x86_64-2.7/bcftools/bin.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/ccall.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/consensus.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/convert.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/csq.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/em.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/filter.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/gvcf.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/hclust.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/kmin.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/main.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/mcall.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/mpileup.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/ploidy.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/prob1.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/regidx.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/rehea
der.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/smpl_ilist.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/tabix.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/tsv2vcf.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/vcfannotate.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/vcfbuf.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/vcfcall.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/vcfcnv.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/vcfconcat.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/vcfconvert.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/vcffilter.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/vcfindex.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/vcfisec.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/vcfmerge.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/vcfnorm.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/vcfplugin.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/vcfquery.c.pysam.o build/temp.linux-x86_64-2.7/bc
ftools/vcfroh.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/vcfsom.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/vcfsort.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/vcfstats.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/vcfview.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/vcmp.c.pysam.o build/temp.linux-x86_64-2.7/bcftools/version.c.pysam.o -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/build/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -L/usr/pkg/lib -lz -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib -lpython2.7 -o build/lib.linux-x86_64-2.7/pysam/libcbcftools.so -Wl,-rpath,$ORIGIN -L/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -Wl,-R/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4
.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib
-skipping 'pysam/libcutils.c' Cython extension (up-to-date)
-building 'pysam.libcutils' extension
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c pysam/libcutils.c -o build/temp.linux-x86_64-2.7/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-pysam/libcutils.c: In function '__pyx_pf_5pysam_9libcutils_8_pysam_dispatch':
-pysam/libcutils.c:6113:3: warning: implicit declaration of function 'bcftools_set_stderr' [-Wimplicit-function-declaration]
- bcftools_set_stderr(__pyx_t_10);
- ^~~~~~~~~~~~~~~~~~~
-pysam/libcutils.c:6285:5: warning: implicit declaration of function 'bcftools_set_stdout_fn' [-Wimplicit-function-declaration]
- bcftools_set_stdout_fn(__pyx_t_13);
- ^~~~~~~~~~~~~~~~~~~~~~
-pysam/libcutils.c:6296:5: warning: implicit declaration of function 'bcftools_set_stdout' [-Wimplicit-function-declaration]
- bcftools_set_stdout(__pyx_t_10);
- ^~~~~~~~~~~~~~~~~~~
-pysam/libcutils.c:7128:5: warning: implicit declaration of function 'bcftools_set_optind' [-Wimplicit-function-declaration]
- bcftools_set_optind(1);
- ^~~~~~~~~~~~~~~~~~~
-pysam/libcutils.c:7207:22: warning: implicit declaration of function 'bcftools_main' [-Wimplicit-function-declaration]
- __pyx_v_retval = bcftools_main((__pyx_v_n + 2), __pyx_v_cargs);
- ^~~~~~~~~~~~~
-pysam/libcutils.c:7276:3: warning: implicit declaration of function 'bcftools_unset_stderr' [-Wimplicit-function-declaration]
- bcftools_unset_stderr();
- ^~~~~~~~~~~~~~~~~~~~~
-pysam/libcutils.c:7312:5: warning: implicit declaration of function 'bcftools_unset_stdout' [-Wimplicit-function-declaration]
- bcftools_unset_stdout();
- ^~~~~~~~~~~~~~~~~~~~~
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c pysam/pysam_util.c -o build/temp.linux-x86_64-2.7/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -shared -L/tmp/pkgbuild/lang/python27/work/Python-2.7.15 -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -pthread -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -Wl,-R/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses build/temp.linux-x86_64-2.7/pysam/libcutils.o build/temp.linux-x86_64-2.7/pysam/pysam_util.o -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -L/usr/pkgsrc/wip/py-pysam/
work/pysam-0.15.1 -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/build/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -L/usr/pkg/lib -lz -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib -lcsamtools -lcbcftools -lpython2.7 -o build/lib.linux-x86_64-2.7/pysam/libcutils.so -Wl,-rpath,$ORIGIN -L/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -Wl,-R/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib
-cythoning pysam/libcalignmentfile.pyx to pysam/libcalignmentfile.c
-building 'pysam.libcalignmentfile' extension
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c pysam/libcalignmentfile.c -o build/temp.linux-x86_64-2.7/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-pysam/libcalignmentfile.c: In function '__pyx_f_5pysam_17libcalignmentfile_14IteratorColumn_cnext':
-pysam/libcalignmentfile.c:30109:126: 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:4:0,
- from pysam/libcalignmentfile.c:573:
-/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib/htslib/sam.h:686:9: 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);
- ^~~~~~~~~~~~~
-pysam/libcalignmentfile.c: In function '__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnext':
-pysam/libcalignmentfile.c:28362:9: warning: ignoring return value of 'bgzf_seek', declared with attribute warn_unused_result [-Wunused-result]
- (void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0));
- ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-pysam/libcalignmentfile.c: In function '__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_open':
-pysam/libcalignmentfile.c:13970:13: warning: ignoring return value of 'sam_hdr_write', declared with attribute warn_unused_result [-Wunused-result]
- (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr));
- ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-cc -shared -L/tmp/pkgbuild/lang/python27/work/Python-2.7.15 -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -pthread -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -Wl,-R/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses build/temp.linux-x86_64-2.7/pysam/libcalignmentfile.o -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -L/usr/pkgsrc/wip/py-
pysam/work/pysam-0.15.1/build/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -L/usr/pkg/lib -lz -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib -lcutils -lpython2.7 -o build/lib.linux-x86_64-2.7/pysam/libcalignmentfile.so -Wl,-rpath,$ORIGIN -L/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -Wl,-R/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib
-skipping 'pysam/libcsamfile.c' Cython extension (up-to-date)
-building 'pysam.libcsamfile' extension
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c pysam/libcsamfile.c -o build/temp.linux-x86_64-2.7/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -shared -L/tmp/pkgbuild/lang/python27/work/Python-2.7.15 -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -pthread -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -Wl,-R/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses build/temp.linux-x86_64-2.7/pysam/libcsamfile.o -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -L/usr/pkgsrc/wip/py-pysam/
work/pysam-0.15.1/build/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -L/usr/pkg/lib -lz -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib -lcutils -lpython2.7 -o build/lib.linux-x86_64-2.7/pysam/libcsamfile.so -Wl,-rpath,$ORIGIN -L/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -Wl,-R/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib
-skipping 'pysam/libcalignedsegment.c' Cython extension (up-to-date)
-building 'pysam.libcalignedsegment' extension
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c pysam/libcalignedsegment.c -o build/temp.linux-x86_64-2.7/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-pysam/libcalignedsegment.c: In function '__pyx_pf_5pysam_18libcalignedsegment_14AlignedSegment_18fromstring':
-pysam/libcalignedsegment.c:14246:3: warning: ignoring return value of 'sam_parse1', declared with attribute warn_unused_result [-Wunused-result]
- (void)(sam_parse1((&__pyx_v_line), __pyx_v_dest->header->ptr, __pyx_v_dest->_delegate));
- ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-cc -shared -L/tmp/pkgbuild/lang/python27/work/Python-2.7.15 -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -pthread -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -Wl,-R/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses build/temp.linux-x86_64-2.7/pysam/libcalignedsegment.o -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -L/usr/pkgsrc/wip/py
-pysam/work/pysam-0.15.1/build/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -L/usr/pkg/lib -lz -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib -lcutils -lpython2.7 -o build/lib.linux-x86_64-2.7/pysam/libcalignedsegment.so -Wl,-rpath,$ORIGIN -L/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -Wl,-R/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib
-skipping 'pysam/libctabix.c' Cython extension (up-to-date)
-building 'pysam.libctabix' extension
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c pysam/libctabix.c -o build/temp.linux-x86_64-2.7/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-pysam/libctabix.c: In function '__pyx_pf_5pysam_9libctabix_9TabixFile_7contigs___get__':
-pysam/libctabix.c:8706:27: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
- __pyx_v_sequences = tbx_seqnames(__pyx_v_self->index, (&__pyx_v_nsequences));
- ^
-In file included from pysam/libctabix.c:580:0:
-pysam/libctabix.c: In function '__pyx_pf_5pysam_9libctabix_4tabix_index':
-/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib/htslib/tbx.h:41:21: warning: overflow in implicit constant conversion [-Woverflow]
- #define TBX_UCSC 0x10000
- ^
-pysam/libctabix.c:13977:39: note: in expansion of macro 'TBX_UCSC'
- __pyx_t_2 = __Pyx_PyInt_From_int8_t(TBX_UCSC); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 975, __pyx_L1_error)
- ^~~~~~~~
-/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib/htslib/tbx.h:41:21: warning: overflow in implicit constant conversion [-Woverflow]
- #define TBX_UCSC 0x10000
- ^
-pysam/libctabix.c:14009:39: 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)
- ^~~~~~~~
-/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib/htslib/tbx.h:41:21: warning: overflow in implicit constant conversion [-Woverflow]
- #define TBX_UCSC 0x10000
- ^
-pysam/libctabix.c:14379:43: 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 -L/tmp/pkgbuild/lang/python27/work/Python-2.7.15 -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -pthread -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -Wl,-R/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses build/temp.linux-x86_64-2.7/pysam/libctabix.o -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -L/usr/pkgsrc/wip/py-pysam/wo
rk/pysam-0.15.1/build/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -L/usr/pkg/lib -lz -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib -lcutils -lpython2.7 -o build/lib.linux-x86_64-2.7/pysam/libctabix.so -Wl,-rpath,$ORIGIN -L/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -Wl,-R/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib
-skipping 'pysam/libcfaidx.c' Cython extension (up-to-date)
-building 'pysam.libcfaidx' extension
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c pysam/libcfaidx.c -o build/temp.linux-x86_64-2.7/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -shared -L/tmp/pkgbuild/lang/python27/work/Python-2.7.15 -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -pthread -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -Wl,-R/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses build/temp.linux-x86_64-2.7/pysam/libcfaidx.o -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -L/usr/pkgsrc/wip/py-pysam/wo
rk/pysam-0.15.1/build/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -L/usr/pkg/lib -lz -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib -lcutils -lpython2.7 -o build/lib.linux-x86_64-2.7/pysam/libcfaidx.so -Wl,-rpath,$ORIGIN -L/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -Wl,-R/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib
-skipping 'pysam/libcbcf.c' Cython extension (up-to-date)
-building 'pysam.libcbcf' extension
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c pysam/libcbcf.c -o build/temp.linux-x86_64-2.7/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-pysam/libcbcf.c: In function '__pyx_pf_5pysam_7libcbcf_13VariantHeader_12__str__':
-pysam/libcbcf.c:33142:3: warning: 'bcf_hdr_fmt_text' is deprecated: use bcf_hdr_format() instead [-Wdeprecated-declarations]
- __pyx_v_hstr = bcf_hdr_fmt_text(__pyx_v_self->ptr, 0, (&__pyx_v_hlen));
- ^~~~~~~~~~~~
-In file included from pysam/htslib_util.h:5:0,
- from pysam/libcbcf.c:572:
-/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib/htslib/vcf.h:439:11: note: declared here
- char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len)
- ^~~~~~~~~~~~~~~~
-cc -shared -L/tmp/pkgbuild/lang/python27/work/Python-2.7.15 -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -pthread -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -Wl,-R/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses build/temp.linux-x86_64-2.7/pysam/libcbcf.o -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -L/usr/pkgsrc/wip/py-pysam/work
/pysam-0.15.1/build/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -L/usr/pkg/lib -lz -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib -lcutils -lpython2.7 -o build/lib.linux-x86_64-2.7/pysam/libcbcf.so -Wl,-rpath,$ORIGIN -L/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -Wl,-R/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib
-skipping 'pysam/libcbgzf.c' Cython extension (up-to-date)
-building 'pysam.libcbgzf' extension
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c pysam/libcbgzf.c -o build/temp.linux-x86_64-2.7/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -shared -L/tmp/pkgbuild/lang/python27/work/Python-2.7.15 -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -pthread -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -Wl,-R/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses build/temp.linux-x86_64-2.7/pysam/libcbgzf.o -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -L/usr/pkgsrc/wip/py-pysam/wor
k/pysam-0.15.1/build/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -L/usr/pkg/lib -lz -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib -lcutils -lpython2.7 -o build/lib.linux-x86_64-2.7/pysam/libcbgzf.so -Wl,-rpath,$ORIGIN -L/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -Wl,-R/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib
-skipping 'pysam/libctabixproxies.c' Cython extension (up-to-date)
-building 'pysam.libctabixproxies' extension
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c pysam/libctabixproxies.c -o build/temp.linux-x86_64-2.7/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -shared -L/tmp/pkgbuild/lang/python27/work/Python-2.7.15 -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -pthread -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -Wl,-R/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses build/temp.linux-x86_64-2.7/pysam/libctabixproxies.o -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -L/usr/pkgsrc/wip/py-p
ysam/work/pysam-0.15.1/build/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -L/usr/pkg/lib -lz -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib -lcutils -lpython2.7 -o build/lib.linux-x86_64-2.7/pysam/libctabixproxies.so -Wl,-rpath,$ORIGIN -L/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -Wl,-R/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib
-skipping 'pysam/libcvcf.c' Cython extension (up-to-date)
-building 'pysam.libcvcf' extension
-cc -DNDEBUG -O2 -D_FORTIFY_SOURCE=2 -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/pkg/include/db4 -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -fPIC -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/htslib -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/samtools/lz4 -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/bcftools -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -I/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -I/usr/pkg/include/python2.7 -c pysam/libcvcf.c -o build/temp.linux-x86_64-2.7/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
-cc -shared -L/tmp/pkgbuild/lang/python27/work/Python-2.7.15 -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -pthread -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -L/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -Wl,-R/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -O2 -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/ncurses build/temp.linux-x86_64-2.7/pysam/libcvcf.o -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/pysam -L/usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1 -L/usr/pkgsrc/wip/py-pysam/work
/pysam-0.15.1/build/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -Lbuild/lib.linux-x86_64-2.7/pysam -L/usr/pkg/lib -lz -llzma -lbz2 -lz -lm -lcurl -lcrypto -lchtslib -lcutils -lpython2.7 -o build/lib.linux-x86_64-2.7/pysam/libcvcf.so -Wl,-rpath,$ORIGIN -L/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -Wl,-R/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib
-===> Installing for py27-pysam-0.15.1
-=> Generating pre-install file lists
-=> Creating installation directories
-(cd /usr/pkgsrc/wip/py-pysam/work/pysam-0.15.1/ && /usr/bin/env PKGSRC_PYTHON_NO_EGG=defined DESTDIR=/usr/pkgsrc/wip/py-pysam/work/.destdir USETOOLS=no PTHREAD_CFLAGS=\ -pthread\ PTHREAD_LDFLAGS=\ -pthread PTHREAD_LIBS=-lpthread\ -lrt PTHREADBASE=/usr DL_CFLAGS= DL_LDFLAGS= DL_LIBS= PYTHON=/usr/pkg/bin/python2.7 CC=cc CFLAGS=-O2\ -D_FORTIFY_SOURCE=2\ -I/usr/include\ -I/usr/pkg/include\ -I/usr/pkg/include/ncurses CPPFLAGS=-I/usr/include\ -I/usr/pkg/include\ -I/usr/pkg/include/ncurses CXX=c++ CXXFLAGS=-O2\ -D_FORTIFY_SOURCE=2\ -I/usr/include\ -I/usr/pkg/include\ -I/usr/pkg/include/ncurses COMPILER_RPATH_FLAG=-Wl,-R F77=gfortran FC=gfortran FFLAGS=-O LANG=C LC_ALL=C LC_COLLATE=C LC_CTYPE=C LC_MESSAGES=C LC_MONETARY=C LC_NUMERIC=C LC_TIME=C LDFLAGS=-L/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so\ -Wl,-R/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so\ -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0\ -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0\ -L/us
r/pkg/gcc6/lib64\ -Wl,-R/usr/pkg/gcc6/lib64\ -L/usr/lib64\ -Wl,-R/usr/lib64\ -L/usr/pkg/lib\ -Wl,-R/usr/pkg/lib LINKER_RPATH_FLAG=-R PATH=/usr/pkgsrc/wip/py-pysam/work/.cwrapper/bin:/usr/pkgsrc/wip/py-pysam/work/.buildlink/bin:/usr/pkgsrc/wip/py-pysam/work/.gcc/bin:/usr/pkgsrc/wip/py-pysam/work/.tools/bin:/usr/pkg/bin:/home/bacon/scripts:/usr/pkg/bin:/usr/local/bin:/home/bacon/scripts:/home/bacon/miniconda3/bin:/usr/pkg/bin:/usr/pkg/sbin:/usr/pkg/gcc5/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/bacon/.local/bin:/home/bacon/bin:/sbin:/usr/sbin:/usr/local/sbin:/usr/pkg/bin:/usr/pkg/bin PREFIX=/usr/pkg MAKELEVEL=0 CONFIG_SITE= PKG_SYSCONFDIR=/usr/pkg/etc CXXCPP=cpp HOME=/usr/pkgsrc/wip/py-pysam/work/.home CWRAPPERS_CONFIG_DIR=/usr/pkgsrc/wip/py-pysam/work/.cwrapper/config CPP=cpp LOCALBASE=/usr/pkg X11BASE=/usr/pkg PKGMANDIR=man PKGINFODIR=info PKGGNUDIR=gnu/ MAKECONF=/dev/null OBJECT_FMT=ELF USETOOLS=no BSD_INSTALL_PROGRAM=/bin/install\ -c\ -s\ -o\ root\ -g\ root\ -m\ 7
55 BSD_INSTALL_SCRIPT=/bin/install\ -c\ -o\ root\ -g\ root\ -m\ 755 BSD_INSTALL_LIB=/bin/install\ -c\ -o\ root\ -g\ root\ -m\ 755 BSD_INSTALL_DATA=/bin/install\ -c\ -o\ root\ -g\ root\ -m\ 644 BSD_INSTALL_MAN=/bin/install\ -c\ -o\ root\ -g\ root\ -m\ 644 BSD_INSTALL=/bin/install BSD_INSTALL_PROGRAM_DIR=/bin/install\ -d\ -o\ root\ -g\ root\ -m\ 755 BSD_INSTALL_SCRIPT_DIR=/bin/install\ -d\ -o\ root\ -g\ root\ -m\ 755 BSD_INSTALL_LIB_DIR=/bin/install\ -d\ -o\ root\ -g\ root\ -m\ 755 BSD_INSTALL_DATA_DIR=/bin/install\ -d\ -o\ root\ -g\ root\ -m\ 755 BSD_INSTALL_MAN_DIR=/bin/install\ -d\ -o\ root\ -g\ root\ -m\ 755 BSD_INSTALL_GAME=/bin/install\ -c\ -s\ -o\ root\ -g\ root\ -m\ 2555 BSD_INSTALL_GAME_DATA=/bin/install\ -c\ -o\ root\ -g\ root\ -m\ 664 BSD_INSTALL_GAME_DIR=/bin/install\ -d\ -o\ root\ -g\ root\ -m\ 775 INSTALL_INFO= MAKEINFO=/usr/pkgsrc/wip/py-pysam/work/.tools/bin/makeinfo FLEX= BISON= PKG_CONFIG= PKG_CONFIG_LIBDIR=/usr/pkgsrc/wip/py-pysam/work/.buildlink/lib64/pkgconfig:/us
r/pkgsrc/wip/py-pysam/work/.buildlink/lib/pkgconfig:/usr/pkgsrc/wip/py-pysam/work/.buildlink/share/pkgconfig PKG_CONFIG_LOG=/usr/pkgsrc/wip/py-pysam/work/.pkg-config.log PKG_CONFIG_PATH= CWRAPPERS_CONFIG_DIR=/usr/pkgsrc/wip/py-pysam/work/.cwrapper/config /usr/pkg/bin/python2.7 setup.py "install" -c -O1 --single-version-externally-managed --root=/usr/pkgsrc/wip/py-pysam/work/.destdir)
-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/pkgsrc/wip/py-pysam/work/.tools/bin/grep
-checking for C compiler warning flags... -Wall
-checking for special C compiler options needed for large files... no
-checking for _FILE_OFFSET_BITS value needed for large files... no
-checking for _LARGEFILE_SOURCE value needed for large files... no
-checking shared library type for unknown-Linux... plain .so
-checking how to run the C preprocessor... cpp
-checking for egrep... /usr/pkgsrc/wip/py-pysam/work/.tools/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... yes
-checking for fdatasync... yes
-checking for library containing log... -lm
-checking for zlib.h... yes
-checking for inflate in -lz... yes
-checking for library containing 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... yes
-checking for CCHmac... no
-checking for library containing HMAC... -lcrypto
-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
-gmake: ./version.sh: Command not found
-gmake: ./version.sh: Command not found
-# pysam: cython is available - using cythonize if necessary
-# pysam: htslib mode is shared
-# pysam: HTSLIB_CONFIGURE_OPTIONS=None
-# pysam: htslib configure options: --enable-libcurl
-# pysam: htslib_config LIBS=-llzma -lbz2 -lz -lm -lcurl -lcrypto
-# pysam: htslib_config PLATFORM=default
-# pysam: htslib_config LIBHTS_OBJS=kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o hfile_libcurl.o hfile_gcs.o hfile_s3.o
-# pysam: htslib_config LDFLAGS=-L/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -Wl,-R/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.so -L/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -Wl,-R/usr/pkg/gcc6/lib/gcc/x86_64-redhat-linux/6.4.0 -L/usr/pkg/gcc6/lib64 -Wl,-R/usr/pkg/gcc6/lib64 -L/usr/lib64 -Wl,-R/usr/lib64 -L/usr/pkg/lib -Wl,-R/usr/pkg/lib
-# pysam: config_option: ENABLE_PLUGINS=0
-# pysam: config_option: HAVE_COMMONCRYPTO=0
-# pysam: config_option: HAVE_GMTIME_R=1
-# pysam: config_option: HAVE_HMAC=1
-# pysam: config_option: HAVE_IRODS=0
-# pysam: config_option: HAVE_LIBCURL=1
-# pysam: config_option: HAVE_MMAP=1
-running install
-running build
-running build_py
-copying pysam/config.py -> build/lib.linux-x86_64-2.7/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 'samtools/win32/__init__.py' not found (or not a regular file)
-package init file 'htslib/__init__.py' not found (or not a regular file)
-package init file 'htslib/htslib/__init__.py' not found (or not a regular file)
-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 /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/Pileup.py -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/__init__.py -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/bcftools.py -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/samtools.py -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/utils.py -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/version.py -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-creating /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include
-copying build/lib.linux-x86_64-2.7/pysam/include/__init__.py -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include
-creating /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools
-copying build/lib.linux-x86_64-2.7/pysam/include/samtools/bam.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools
-copying build/lib.linux-x86_64-2.7/pysam/include/samtools/bam2bcf.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools
-copying build/lib.linux-x86_64-2.7/pysam/include/samtools/bam_endian.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools
-copying build/lib.linux-x86_64-2.7/pysam/include/samtools/bam_lpileup.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools
-copying build/lib.linux-x86_64-2.7/pysam/include/samtools/bam_plbuf.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools
-copying build/lib.linux-x86_64-2.7/pysam/include/samtools/bedidx.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools
-copying build/lib.linux-x86_64-2.7/pysam/include/samtools/sam.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools
-copying build/lib.linux-x86_64-2.7/pysam/include/samtools/sam_header.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools
-copying build/lib.linux-x86_64-2.7/pysam/include/samtools/sam_opts.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools
-copying build/lib.linux-x86_64-2.7/pysam/include/samtools/sample.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools
-copying build/lib.linux-x86_64-2.7/pysam/include/samtools/samtools.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools
-copying build/lib.linux-x86_64-2.7/pysam/include/samtools/samtools.pysam.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools
-copying build/lib.linux-x86_64-2.7/pysam/include/samtools/stats_isize.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools
-copying build/lib.linux-x86_64-2.7/pysam/include/samtools/tmp_file.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools
-copying build/lib.linux-x86_64-2.7/pysam/include/samtools/version.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools
-copying build/lib.linux-x86_64-2.7/pysam/include/samtools/config.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools
-creating /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools/win32
-copying build/lib.linux-x86_64-2.7/pysam/include/samtools/win32/xcurses.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools/win32
-copying build/lib.linux-x86_64-2.7/pysam/include/samtools/win32/zconf.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools/win32
-copying build/lib.linux-x86_64-2.7/pysam/include/samtools/win32/zlib.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools/win32
-creating /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools
-copying build/lib.linux-x86_64-2.7/pysam/include/bcftools/HMM.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools
-copying build/lib.linux-x86_64-2.7/pysam/include/bcftools/bam2bcf.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools
-copying build/lib.linux-x86_64-2.7/pysam/include/bcftools/bam_sample.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools
-copying build/lib.linux-x86_64-2.7/pysam/include/bcftools/bcftools.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools
-copying build/lib.linux-x86_64-2.7/pysam/include/bcftools/bcftools.pysam.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools
-copying build/lib.linux-x86_64-2.7/pysam/include/bcftools/bin.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools
-copying build/lib.linux-x86_64-2.7/pysam/include/bcftools/call.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools
-copying build/lib.linux-x86_64-2.7/pysam/include/bcftools/convert.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools
-copying build/lib.linux-x86_64-2.7/pysam/include/bcftools/filter.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools
-copying build/lib.linux-x86_64-2.7/pysam/include/bcftools/gvcf.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools
-copying build/lib.linux-x86_64-2.7/pysam/include/bcftools/hclust.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools
-copying build/lib.linux-x86_64-2.7/pysam/include/bcftools/khash_str2str.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools
-copying build/lib.linux-x86_64-2.7/pysam/include/bcftools/kheap.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools
-copying build/lib.linux-x86_64-2.7/pysam/include/bcftools/kmin.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools
-copying build/lib.linux-x86_64-2.7/pysam/include/bcftools/mw.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools
-copying build/lib.linux-x86_64-2.7/pysam/include/bcftools/ploidy.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools
-copying build/lib.linux-x86_64-2.7/pysam/include/bcftools/prob1.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools
-copying build/lib.linux-x86_64-2.7/pysam/include/bcftools/rbuf.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools
-copying build/lib.linux-x86_64-2.7/pysam/include/bcftools/regidx.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools
-copying build/lib.linux-x86_64-2.7/pysam/include/bcftools/smpl_ilist.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools
-copying build/lib.linux-x86_64-2.7/pysam/include/bcftools/tsv2vcf.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools
-copying build/lib.linux-x86_64-2.7/pysam/include/bcftools/vcfbuf.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools
-copying build/lib.linux-x86_64-2.7/pysam/include/bcftools/vcmp.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools
-copying build/lib.linux-x86_64-2.7/pysam/include/bcftools/version.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools
-copying build/lib.linux-x86_64-2.7/pysam/include/bcftools/config.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools
-creating /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib
-copying build/lib.linux-x86_64-2.7/pysam/include/htslib/bcf_sr_sort.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib
-copying build/lib.linux-x86_64-2.7/pysam/include/htslib/hfile_internal.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib
-copying build/lib.linux-x86_64-2.7/pysam/include/htslib/hts_internal.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib
-copying build/lib.linux-x86_64-2.7/pysam/include/htslib/textutils_internal.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib
-copying build/lib.linux-x86_64-2.7/pysam/include/htslib/thread_pool_internal.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib
-copying build/lib.linux-x86_64-2.7/pysam/include/htslib/version.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib
-copying build/lib.linux-x86_64-2.7/pysam/include/htslib/config.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib
-creating /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib
-copying build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib/bgzf.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib
-copying build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib/cram.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib
-copying build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib/faidx.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib
-copying build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib/hfile.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib
-copying build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib/hts.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib
-copying build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib/hts_defs.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib
-copying build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib/hts_endian.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib
-copying build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib/hts_log.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib
-copying build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib/hts_os.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib
-copying build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib/kbitset.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib
-copying build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib/kfunc.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib
-copying build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib/khash.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib
-copying build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib/khash_str2int.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib
-copying build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib/klist.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib
-copying build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib/knetfile.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib
-copying build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib/kseq.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib
-copying build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib/ksort.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib
-copying build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib/kstring.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib
-copying build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib/regidx.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib
-copying build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib/sam.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib
-copying build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib/synced_bcf_reader.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib
-copying build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib/tbx.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib
-copying build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib/thread_pool.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib
-copying build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib/vcf.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib
-copying build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib/vcf_sweep.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib
-copying build/lib.linux-x86_64-2.7/pysam/include/htslib/htslib/vcfutils.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib
-copying build/lib.linux-x86_64-2.7/pysam/libcalignedsegment.pxd -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/libcalignmentfile.pxd -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/libcbcf.pxd -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/libcbcftools.pxd -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/libcfaidx.pxd -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/libchtslib.pxd -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/libcsamfile.pxd -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/libcsamtools.pxd -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/libctabix.pxd -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/libctabixproxies.pxd -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/libcutils.pxd -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/libcvcf.pxd -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/cbcftools_util.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/csamtools_util.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/htslib_util.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/pysam_stream.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/pysam_util.h -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/libchtslib.so -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/libcsamtools.so -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/libcbcftools.so -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/libcutils.so -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/libcalignmentfile.so -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/libcsamfile.so -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/libcalignedsegment.so -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/libctabix.so -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/libcfaidx.so -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/libcbcf.so -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/libcbgzf.so -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/libctabixproxies.so -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/libcvcf.so -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-copying build/lib.linux-x86_64-2.7/pysam/config.py -> /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam
-byte-compiling /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/Pileup.py to Pileup.pyc
-byte-compiling /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/__init__.py to __init__.pyc
-byte-compiling /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/bcftools.py to bcftools.pyc
-byte-compiling /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/samtools.py to samtools.pyc
-byte-compiling /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/utils.py to utils.pyc
-byte-compiling /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/version.py to version.pyc
-byte-compiling /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/__init__.py to __init__.pyc
-byte-compiling /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/config.py to config.pyc
-writing byte-compilation script '/tmp/tmpvIol_2.py'
-/usr/pkg/bin/python2.7 -O /tmp/tmpvIol_2.py
-removing /tmp/tmpvIol_2.py
-running install_egg_info
-running egg_info
-writing pysam.egg-info/PKG-INFO
-writing top-level names to pysam.egg-info/top_level.txt
-writing dependency_links to pysam.egg-info/dependency_links.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/win/*.c'
-warning: no files found matching 'htslib/win/*.h'
-writing manifest file 'pysam.egg-info/SOURCES.txt'
-Copying pysam.egg-info to /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam-0.15.1-py2.7.egg-info
-running install_scripts
-=> Automatic manual page handling
-=> Generating post-install file lists
-if test -d "/usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam-0.15.1-py2.7.egg-info"; then /usr/bin/find /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam-0.15.1-py2.7.egg-info -type f -exec /bin/chmod 644 '{}' +; fi
-=> Checking file-check results for py27-pysam-0.15.1
-=> Checking for non-existent script interpreters in py27-pysam-0.15.1
-=> Checking file permissions in py27-pysam-0.15.1
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/cbcftools_util.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/csamtools_util.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/htslib_util.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools/bam2bcf.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools/bam_sample.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools/bcftools.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools/bcftools.pysam.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools/bin.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools/call.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools/convert.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools/filter.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools/gvcf.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools/hclust.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools/HMM.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools/khash_str2str.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools/kheap.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools/kmin.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools/mw.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools/ploidy.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools/prob1.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools/rbuf.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools/regidx.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools/smpl_ilist.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools/tsv2vcf.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools/vcfbuf.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools/vcmp.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/bcftools/version.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/bcf_sr_sort.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/hfile_internal.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/hts_internal.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib/bgzf.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib/cram.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib/faidx.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib/hfile.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib/hts_defs.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib/hts_endian.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib/hts.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib/hts_log.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib/hts_os.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib/kbitset.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib/kfunc.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib/khash.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib/khash_str2int.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib/klist.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib/knetfile.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib/kseq.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib/ksort.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib/kstring.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib/regidx.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib/sam.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib/synced_bcf_reader.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib/tbx.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib/thread_pool.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib/vcf.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib/vcf_sweep.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/htslib/vcfutils.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/textutils_internal.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/thread_pool_internal.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/htslib/version.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools/bam2bcf.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools/bam_endian.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools/bam.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools/bam_lpileup.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools/bam_plbuf.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools/bedidx.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools/sam.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools/sam_header.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools/sam_opts.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools/sample.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools/samtools.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools/samtools.pysam.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools/stats_isize.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools/tmp_file.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools/version.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools/win32/xcurses.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools/win32/zconf.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/include/samtools/win32/zlib.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/libcalignedsegment.pxd: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/libcalignmentfile.pxd: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/libcbcf.pxd: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/libcbcftools.pxd: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/libcfaidx.pxd: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/libchtslib.pxd: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/libcsamfile.pxd: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/libcsamtools.pxd: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/libctabixproxies.pxd: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/libctabix.pxd: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/libcutils.pxd: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/libcvcf.pxd: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/pysam_stream.h: group-writable file.
-warning: /usr/pkgsrc/wip/py-pysam/work/.destdir/usr/pkg/lib/python2.7/site-packages/pysam/pysam_util.h: group-writable file.
-0 errors and 91 warnings.
-=> Checking for missing run-time search paths in py27-pysam-0.15.1
-ERROR: lib/python2.7/site-packages/pysam/libcalignedsegment.so: missing library: libcutils.so
-ERROR: lib/python2.7/site-packages/pysam/libcalignedsegment.so: missing library: libchtslib.so
-ERROR: lib/python2.7/site-packages/pysam/libcalignmentfile.so: missing library: libcutils.so
-ERROR: lib/python2.7/site-packages/pysam/libcalignmentfile.so: missing library: libchtslib.so
-ERROR: lib/python2.7/site-packages/pysam/libcbcf.so: missing library: libcutils.so
-ERROR: lib/python2.7/site-packages/pysam/libcbcf.so: missing library: libchtslib.so
-ERROR: lib/python2.7/site-packages/pysam/libcbcftools.so: missing library: libchtslib.so
-ERROR: lib/python2.7/site-packages/pysam/libcbgzf.so: missing library: libcutils.so
-ERROR: lib/python2.7/site-packages/pysam/libcbgzf.so: missing library: libchtslib.so
-ERROR: lib/python2.7/site-packages/pysam/libcfaidx.so: missing library: libcutils.so
-ERROR: lib/python2.7/site-packages/pysam/libcfaidx.so: missing library: libchtslib.so
-ERROR: lib/python2.7/site-packages/pysam/libcsamfile.so: missing library: libcutils.so
-ERROR: lib/python2.7/site-packages/pysam/libcsamfile.so: missing library: libchtslib.so
-ERROR: lib/python2.7/site-packages/pysam/libcsamtools.so: missing library: libchtslib.so
-ERROR: lib/python2.7/site-packages/pysam/libctabix.so: missing library: libcutils.so
-ERROR: lib/python2.7/site-packages/pysam/libctabix.so: missing library: libchtslib.so
-ERROR: lib/python2.7/site-packages/pysam/libctabixproxies.so: missing library: libcutils.so
-ERROR: lib/python2.7/site-packages/pysam/libctabixproxies.so: missing library: libchtslib.so
-ERROR: lib/python2.7/site-packages/pysam/libcutils.so: missing library: libcbcftools.so
-ERROR: lib/python2.7/site-packages/pysam/libcutils.so: missing library: libcsamtools.so
-ERROR: lib/python2.7/site-packages/pysam/libcutils.so: missing library: libchtslib.so
-ERROR: lib/python2.7/site-packages/pysam/libcvcf.so: missing library: libcutils.so
-ERROR: lib/python2.7/site-packages/pysam/libcvcf.so: missing library: libchtslib.so
-*** Error code 1
-
-Stop.
-bmake.bin[1]: stopped in /usr/pkgsrc/wip/py-pysam
-*** Error code 1
-
-Stop.
-bmake.bin: stopped in /usr/pkgsrc/wip/py-pysam
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