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py-pysam: Python module for reading, manipulating and writing genomic data
Module Name: pkgsrc-wip
Committed By: Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By: outpaddling
Date: Mon Nov 5 14:26:18 2018 -0600
Changeset: 7bd933595eb60b47f50f01923db096a60e245337
Modified Files:
Makefile
Added Files:
py-pysam/DESCR
py-pysam/Makefile
py-pysam/PLIST
py-pysam/distinfo
py-pysam/log
py-pysam/patches/patch-setup.py
Log Message:
py-pysam: Python module for reading, manipulating and writing genomic data
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=7bd933595eb60b47f50f01923db096a60e245337
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
Makefile | 1 +
py-pysam/DESCR | 7 +
py-pysam/Makefile | 33 ++
py-pysam/PLIST | 137 ++++++
py-pysam/distinfo | 7 +
py-pysam/log | 908 ++++++++++++++++++++++++++++++++++++++++
py-pysam/patches/patch-setup.py | 15 +
7 files changed, 1108 insertions(+)
diffs:
diff --git a/Makefile b/Makefile
index a1609aa750..8e40ec7344 100644
--- a/Makefile
+++ b/Makefile
@@ -3715,6 +3715,7 @@ SUBDIR+= py-pyquante
SUBDIR+= py-pyrit
SUBDIR+= py-pyrr
SUBDIR+= py-pysal
+SUBDIR+= py-pysam
SUBDIR+= py-pysaml2
SUBDIR+= py-pysb
SUBDIR+= py-pyscard
diff --git a/py-pysam/DESCR b/py-pysam/DESCR
new file mode 100644
index 0000000000..d1c2f53ef9
--- /dev/null
+++ b/py-pysam/DESCR
@@ -0,0 +1,7 @@
+pysam is a lightweight wrapper of the htslib C-API and provides facilities to
+read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access
+to the command line functionality of the samtools and bcftools packages. The
+module supports compression and random access through indexing.
+This module provides a low-level wrapper around the htslib C-API as using
+cython and a high-level API for convenient access to the data within standard
+genomic file formats.
diff --git a/py-pysam/Makefile b/py-pysam/Makefile
new file mode 100644
index 0000000000..907e8fa7b8
--- /dev/null
+++ b/py-pysam/Makefile
@@ -0,0 +1,33 @@
+# $NetBSD$
+#
+###########################################################
+# Generated by fbsd2pkg #
+# Mon Nov 5 13:27:01 CST 2018 #
+###########################################################
+
+DISTNAME= pysam-${PV}
+PKGNAME= ${PYPKGPREFIX}-pysam-${PV}
+CATEGORIES= biology
+MASTER_SITES= ${MASTER_SITE_PYPI:=p/pysam/}
+
+MAINTAINER= bacon%NetBSD.org@localhost
+HOMEPAGE= https://github.com/pysam-developers/pysam
+COMMENT= Python module for reading, manipulating and writing genomic data sets
+LICENSE= mit
+
+USE_TOOLS+= gmake
+
+# Succeed in altering link commands, but do not help
+# LDFLAGS+= -L${PREFIX}/lib/python2.7/site-packages/pysam/libcutils.so
+# LDFLAGS+= ${COMPILER_RPATH_FLAG}${PREFIX}/lib/python2.7/site-packages/pysam/libcutils.so
+
+PV= 0.15.1
+
+.include "../../lang/python/egg.mk"
+.include "../../devel/ncurses/buildlink3.mk"
+.include "../../devel/py-cython/buildlink3.mk"
+.include "../../www/curl/buildlink3.mk"
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../archivers/bzip2/buildlink3.mk"
+.include "../../archivers/xz/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/py-pysam/PLIST b/py-pysam/PLIST
new file mode 100644
index 0000000000..e0aa924cb7
--- /dev/null
+++ b/py-pysam/PLIST
@@ -0,0 +1,137 @@
+@comment $NetBSD$
+${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
+${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
+${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
+${PYSITELIB}/${EGG_INFODIR}/not-zip-safe
+${PYSITELIB}/${EGG_INFODIR}/top_level.txt
+${PYSITELIB}/pysam/Pileup.py
+${PYSITELIB}/pysam/Pileup.pyc
+${PYSITELIB}/pysam/Pileup.pyo
+${PYSITELIB}/pysam/__init__.py
+${PYSITELIB}/pysam/__init__.pyc
+${PYSITELIB}/pysam/__init__.pyo
+${PYSITELIB}/pysam/bcftools.py
+${PYSITELIB}/pysam/bcftools.pyc
+${PYSITELIB}/pysam/bcftools.pyo
+${PYSITELIB}/pysam/cbcftools_util.h
+${PYSITELIB}/pysam/config.py
+${PYSITELIB}/pysam/config.pyc
+${PYSITELIB}/pysam/config.pyo
+${PYSITELIB}/pysam/csamtools_util.h
+${PYSITELIB}/pysam/htslib_util.h
+${PYSITELIB}/pysam/include/__init__.py
+${PYSITELIB}/pysam/include/__init__.pyc
+${PYSITELIB}/pysam/include/__init__.pyo
+${PYSITELIB}/pysam/include/bcftools/HMM.h
+${PYSITELIB}/pysam/include/bcftools/bam2bcf.h
+${PYSITELIB}/pysam/include/bcftools/bam_sample.h
+${PYSITELIB}/pysam/include/bcftools/bcftools.h
+${PYSITELIB}/pysam/include/bcftools/bcftools.pysam.h
+${PYSITELIB}/pysam/include/bcftools/bin.h
+${PYSITELIB}/pysam/include/bcftools/call.h
+${PYSITELIB}/pysam/include/bcftools/config.h
+${PYSITELIB}/pysam/include/bcftools/convert.h
+${PYSITELIB}/pysam/include/bcftools/filter.h
+${PYSITELIB}/pysam/include/bcftools/gvcf.h
+${PYSITELIB}/pysam/include/bcftools/hclust.h
+${PYSITELIB}/pysam/include/bcftools/khash_str2str.h
+${PYSITELIB}/pysam/include/bcftools/kheap.h
+${PYSITELIB}/pysam/include/bcftools/kmin.h
+${PYSITELIB}/pysam/include/bcftools/mw.h
+${PYSITELIB}/pysam/include/bcftools/ploidy.h
+${PYSITELIB}/pysam/include/bcftools/prob1.h
+${PYSITELIB}/pysam/include/bcftools/rbuf.h
+${PYSITELIB}/pysam/include/bcftools/regidx.h
+${PYSITELIB}/pysam/include/bcftools/smpl_ilist.h
+${PYSITELIB}/pysam/include/bcftools/tsv2vcf.h
+${PYSITELIB}/pysam/include/bcftools/vcfbuf.h
+${PYSITELIB}/pysam/include/bcftools/vcmp.h
+${PYSITELIB}/pysam/include/bcftools/version.h
+${PYSITELIB}/pysam/include/htslib/bcf_sr_sort.h
+${PYSITELIB}/pysam/include/htslib/config.h
+${PYSITELIB}/pysam/include/htslib/hfile_internal.h
+${PYSITELIB}/pysam/include/htslib/hts_internal.h
+${PYSITELIB}/pysam/include/htslib/htslib/bgzf.h
+${PYSITELIB}/pysam/include/htslib/htslib/cram.h
+${PYSITELIB}/pysam/include/htslib/htslib/faidx.h
+${PYSITELIB}/pysam/include/htslib/htslib/hfile.h
+${PYSITELIB}/pysam/include/htslib/htslib/hts.h
+${PYSITELIB}/pysam/include/htslib/htslib/hts_defs.h
+${PYSITELIB}/pysam/include/htslib/htslib/hts_endian.h
+${PYSITELIB}/pysam/include/htslib/htslib/hts_log.h
+${PYSITELIB}/pysam/include/htslib/htslib/hts_os.h
+${PYSITELIB}/pysam/include/htslib/htslib/kbitset.h
+${PYSITELIB}/pysam/include/htslib/htslib/kfunc.h
+${PYSITELIB}/pysam/include/htslib/htslib/khash.h
+${PYSITELIB}/pysam/include/htslib/htslib/khash_str2int.h
+${PYSITELIB}/pysam/include/htslib/htslib/klist.h
+${PYSITELIB}/pysam/include/htslib/htslib/knetfile.h
+${PYSITELIB}/pysam/include/htslib/htslib/kseq.h
+${PYSITELIB}/pysam/include/htslib/htslib/ksort.h
+${PYSITELIB}/pysam/include/htslib/htslib/kstring.h
+${PYSITELIB}/pysam/include/htslib/htslib/regidx.h
+${PYSITELIB}/pysam/include/htslib/htslib/sam.h
+${PYSITELIB}/pysam/include/htslib/htslib/synced_bcf_reader.h
+${PYSITELIB}/pysam/include/htslib/htslib/tbx.h
+${PYSITELIB}/pysam/include/htslib/htslib/thread_pool.h
+${PYSITELIB}/pysam/include/htslib/htslib/vcf.h
+${PYSITELIB}/pysam/include/htslib/htslib/vcf_sweep.h
+${PYSITELIB}/pysam/include/htslib/htslib/vcfutils.h
+${PYSITELIB}/pysam/include/htslib/textutils_internal.h
+${PYSITELIB}/pysam/include/htslib/thread_pool_internal.h
+${PYSITELIB}/pysam/include/htslib/version.h
+${PYSITELIB}/pysam/include/samtools/bam.h
+${PYSITELIB}/pysam/include/samtools/bam2bcf.h
+${PYSITELIB}/pysam/include/samtools/bam_endian.h
+${PYSITELIB}/pysam/include/samtools/bam_lpileup.h
+${PYSITELIB}/pysam/include/samtools/bam_plbuf.h
+${PYSITELIB}/pysam/include/samtools/bedidx.h
+${PYSITELIB}/pysam/include/samtools/config.h
+${PYSITELIB}/pysam/include/samtools/sam.h
+${PYSITELIB}/pysam/include/samtools/sam_header.h
+${PYSITELIB}/pysam/include/samtools/sam_opts.h
+${PYSITELIB}/pysam/include/samtools/sample.h
+${PYSITELIB}/pysam/include/samtools/samtools.h
+${PYSITELIB}/pysam/include/samtools/samtools.pysam.h
+${PYSITELIB}/pysam/include/samtools/stats_isize.h
+${PYSITELIB}/pysam/include/samtools/tmp_file.h
+${PYSITELIB}/pysam/include/samtools/version.h
+${PYSITELIB}/pysam/include/samtools/win32/xcurses.h
+${PYSITELIB}/pysam/include/samtools/win32/zconf.h
+${PYSITELIB}/pysam/include/samtools/win32/zlib.h
+${PYSITELIB}/pysam/libcalignedsegment.pxd
+${PYSITELIB}/pysam/libcalignedsegment.so
+${PYSITELIB}/pysam/libcalignmentfile.pxd
+${PYSITELIB}/pysam/libcalignmentfile.so
+${PYSITELIB}/pysam/libcbcf.pxd
+${PYSITELIB}/pysam/libcbcf.so
+${PYSITELIB}/pysam/libcbcftools.pxd
+${PYSITELIB}/pysam/libcbcftools.so
+${PYSITELIB}/pysam/libcbgzf.so
+${PYSITELIB}/pysam/libcfaidx.pxd
+${PYSITELIB}/pysam/libcfaidx.so
+${PYSITELIB}/pysam/libchtslib.pxd
+${PYSITELIB}/pysam/libchtslib.so
+${PYSITELIB}/pysam/libcsamfile.pxd
+${PYSITELIB}/pysam/libcsamfile.so
+${PYSITELIB}/pysam/libcsamtools.pxd
+${PYSITELIB}/pysam/libcsamtools.so
+${PYSITELIB}/pysam/libctabix.pxd
+${PYSITELIB}/pysam/libctabix.so
+${PYSITELIB}/pysam/libctabixproxies.pxd
+${PYSITELIB}/pysam/libctabixproxies.so
+${PYSITELIB}/pysam/libcutils.pxd
+${PYSITELIB}/pysam/libcutils.so
+${PYSITELIB}/pysam/libcvcf.pxd
+${PYSITELIB}/pysam/libcvcf.so
+${PYSITELIB}/pysam/pysam_stream.h
+${PYSITELIB}/pysam/pysam_util.h
+${PYSITELIB}/pysam/samtools.py
+${PYSITELIB}/pysam/samtools.pyc
+${PYSITELIB}/pysam/samtools.pyo
+${PYSITELIB}/pysam/utils.py
+${PYSITELIB}/pysam/utils.pyc
+${PYSITELIB}/pysam/utils.pyo
+${PYSITELIB}/pysam/version.py
+${PYSITELIB}/pysam/version.pyc
+${PYSITELIB}/pysam/version.pyo
diff --git a/py-pysam/distinfo b/py-pysam/distinfo
new file mode 100644
index 0000000000..1bf099d160
--- /dev/null
+++ b/py-pysam/distinfo
@@ -0,0 +1,7 @@
+$NetBSD$
+
+SHA1 (pysam-0.15.1.tar.gz) = e44068afc7520d211f4537873a963f16a6e53a8f
+RMD160 (pysam-0.15.1.tar.gz) = f44ed399f80325bb084d254a3d16d97c6bc25f0f
+SHA512 (pysam-0.15.1.tar.gz) = 12f2b20e81554e47135a81d4d627b8130cb09645ba76bfe69826a9e1c052a4e2750eef3fc08538801b6da9e712bcf0fbdf9155700592ad25030a805b0228dda6
+Size (pysam-0.15.1.tar.gz) = 3220356 bytes
+SHA1 (patch-setup.py) = 368c4b99c1f8103d34096145f7badd9310736554
diff --git a/py-pysam/log b/py-pysam/log
new file mode 100644
index 0000000000..6380c72c50
--- /dev/null
+++ b/py-pysam/log
@@ -0,0 +1,908 @@
+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
diff --git a/py-pysam/patches/patch-setup.py b/py-pysam/patches/patch-setup.py
new file mode 100644
index 0000000000..9231af0479
--- /dev/null
+++ b/py-pysam/patches/patch-setup.py
@@ -0,0 +1,15 @@
+$NetBSD$
+
+# Portability
+
+--- setup.py.orig 2017-04-19 05:48:10 UTC
++++ setup.py
+@@ -60,7 +60,7 @@ def run_configure(option):
+
+
+ def run_make_print_config():
+- stdout = subprocess.check_output(["make", "-s", "print-config"])
++ stdout = subprocess.check_output(["gmake", "-s", "print-config"])
+ if IS_PYTHON3:
+ stdout = stdout.decode("ascii")
+
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