printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild pysam-py27 2>&1 The package 'pysam-py27' will be built without being installed. Reading build dependency for pysam-py27-0.7.5-1... Reading dependency for pysam-py27-0.7.5-1... Reading build conflict for pysam-py27-0.7.5-1... The package 'setuptools-tng-py27' will be installed. Reading dependency for setuptools-tng-py27-5.1-1... Reading runtime dependency for setuptools-tng-py27-5.1-1... The package 'python27' will be installed. Reading dependency for python27-2.7.8-1... Reading runtime dependency for python27-2.7.8-1... The package 'samtools' will be installed. Reading dependency for samtools-0.1.19-2... Reading runtime dependency for samtools-0.1.19-2... The package 'python27-shlibs' will be installed. Reading dependency for python27-shlibs-2.7.8-1... Reading runtime dependency for python27-shlibs-2.7.8-1... The package 'blt-shlibs' will be installed. Reading dependency for blt-shlibs-2.4z-160... Reading runtime dependency for blt-shlibs-2.4z-160... The package 'db53-aes-shlibs' will be installed. Reading dependency for db53-aes-shlibs-5.3.21-2... Reading runtime dependency for db53-aes-shlibs-5.3.21-2... The package 'expat1-shlibs' will be installed. Reading dependency for expat1-shlibs-2.1.0-1... Reading runtime dependency for expat1-shlibs-2.1.0-1... The package 'gdbm3-shlibs' will be installed. Reading dependency for gdbm3-shlibs-1.8.3-4... Reading runtime dependency for gdbm3-shlibs-1.8.3-4... The package 'libffi6-shlibs' will be installed. Reading dependency for libffi6-shlibs-3.1-1... Reading runtime dependency for libffi6-shlibs-3.1-1... The package 'openssl100-shlibs' will be installed. Reading dependency for openssl100-shlibs-1.0.1h-1... Reading runtime dependency for openssl100-shlibs-1.0.1h-1... The package 'sqlite3-shlibs' will be installed. Reading dependency for sqlite3-shlibs-3.8.3.1-1... Reading runtime dependency for sqlite3-shlibs-3.8.3.1-1... The package 'tcltk' will be installed. Reading dependency for tcltk-8.6.1-104... Reading runtime dependency for tcltk-8.6.1-104... The package 'tcltk-shlibs' will be installed. Reading dependency for tcltk-shlibs-8.6.1-104... Reading runtime dependency for tcltk-shlibs-8.6.1-104... The package 'fontconfig2-shlibs' will be installed. Reading dependency for fontconfig2-shlibs-2.10.2-1... Reading runtime dependency for fontconfig2-shlibs-2.10.2-1... The package 'xft2-shlibs' will be installed. Reading dependency for xft2-shlibs-2.2.0-3... Reading runtime dependency for xft2-shlibs-2.2.0-3... The package 'fontconfig-config' will be installed. Reading dependency for fontconfig-config-2.10.2-1... Reading runtime dependency for fontconfig-config-2.10.2-1... The following package will be rebuilt: pysam-py27 The following 16 additional packages will be installed: blt-shlibs db53-aes-shlibs expat1-shlibs fontconfig-config fontconfig2-shlibs gdbm3-shlibs libffi6-shlibs openssl100-shlibs python27 python27-shlibs samtools setuptools-tng-py27 sqlite3-shlibs tcltk tcltk-shlibs xft2-shlibs Do you want to continue? [Y/n] (assuming default) curl --connect-timeout 30 -f -L -A 'fink/0.37.0' -O http://distfiles.master.finkmirrors.net/distfiles/pysam-0.7.5.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 38 1432k 38 551k 0 0 571k 0 0:00:02 --:--:-- 0:00:02 570k 100 1432k 100 1432k 0 0 890k 0 0:00:01 0:00:01 --:--:-- 891k Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/crypto/db53-aes-shlibs_5.3.21-2_darwin-x86_64.deb Selecting previously deselected package db53-aes-shlibs. (Reading database ... 4688 files and directories currently installed.) Unpacking db53-aes-shlibs (from .../db53-aes-shlibs_5.3.21-2_darwin-x86_64.deb) ... Setting up db53-aes-shlibs (5.3.21-2) ... Clearing dependency_libs of .la files being installed Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/base/expat1-shlibs_2.1.0-1_darwin-x86_64.deb Selecting previously deselected package expat1-shlibs. (Reading database ... 4698 files and directories currently installed.) Unpacking expat1-shlibs (from .../expat1-shlibs_2.1.0-1_darwin-x86_64.deb) ... Setting up expat1-shlibs (2.1.0-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/x11/fontconfig2-shlibs_2.10.2-1_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/x11/fontconfig-config_2.10.2-1_darwin-x86_64.deb Selecting previously deselected package fontconfig2-shlibs. (Reading database ... 4703 files and directories currently installed.) Unpacking fontconfig2-shlibs (from .../fontconfig2-shlibs_2.10.2-1_darwin-x86_64.deb) ... Selecting previously deselected package fontconfig-config. Unpacking fontconfig-config (from .../fontconfig-config_2.10.2-1_darwin-x86_64.deb) ... Setting up fontconfig-config (2.10.2-1) ... Setting up fontconfig2-shlibs (2.10.2-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/gdbm3-shlibs_1.8.3-4_darwin-x86_64.deb Selecting previously deselected package gdbm3-shlibs. (Reading database ... 4788 files and directories currently installed.) Unpacking gdbm3-shlibs (from .../gdbm3-shlibs_1.8.3-4_darwin-x86_64.deb) ... Setting up gdbm3-shlibs (1.8.3-4) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/libffi6-shlibs_3.1-1_darwin-x86_64.deb Selecting previously deselected package libffi6-shlibs. (Reading database ... 4796 files and directories currently installed.) Unpacking libffi6-shlibs (from .../libffi6-shlibs_3.1-1_darwin-x86_64.deb) ... Setting up libffi6-shlibs (3.1-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/base/openssl100-shlibs_1.0.1h-1_darwin-x86_64.deb Selecting previously deselected package openssl100-shlibs. (Reading database ... 4797 files and directories currently installed.) Unpacking openssl100-shlibs (from .../openssl100-shlibs_1.0.1h-1_darwin-x86_64.deb) ... Setting up openssl100-shlibs (1.0.1h-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/samtools_0.1.19-2_darwin-x86_64.deb Selecting previously deselected package samtools. (Reading database ... 4818 files and directories currently installed.) Unpacking samtools (from .../samtools_0.1.19-2_darwin-x86_64.deb) ... Setting up samtools (0.1.19-2) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/database/sqlite3-shlibs_3.8.3.1-1_darwin-x86_64.deb Selecting previously deselected package sqlite3-shlibs. (Reading database ... 4847 files and directories currently installed.) Unpacking sqlite3-shlibs (from .../sqlite3-shlibs_3.8.3.1-1_darwin-x86_64.deb) ... Setting up sqlite3-shlibs (3.8.3.1-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/x11/xft2-shlibs_2.2.0-3_darwin-x86_64.deb Selecting previously deselected package xft2-shlibs. (Reading database ... 4851 files and directories currently installed.) Unpacking xft2-shlibs (from .../xft2-shlibs_2.2.0-3_darwin-x86_64.deb) ... Setting up xft2-shlibs (2.2.0-3) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/tcltk_8.6.1-104_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/languages/tcltk-shlibs_8.6.1-104_darwin-x86_64.deb Selecting previously deselected package tcltk. (Reading database ... 4860 files and directories currently installed.) Unpacking tcltk (from .../tcltk_8.6.1-104_darwin-x86_64.deb) ... Selecting previously deselected package tcltk-shlibs. Unpacking tcltk-shlibs (from .../tcltk-shlibs_8.6.1-104_darwin-x86_64.deb) ... Setting up tcltk-shlibs (8.6.1-104) ... Setting up tcltk (8.6.1-104) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/x11/blt-shlibs_2.4z-160_darwin-x86_64.deb Selecting previously deselected package blt-shlibs. (Reading database ... 5335 files and directories currently installed.) Unpacking blt-shlibs (from .../blt-shlibs_2.4z-160_darwin-x86_64.deb) ... Setting up blt-shlibs (2.4z-160) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/python27_2.7.8-1_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/languages/python27-shlibs_2.7.8-1_darwin-x86_64.deb Selecting previously deselected package python27. (Reading database ... 5341 files and directories currently installed.) Unpacking python27 (from .../python27_2.7.8-1_darwin-x86_64.deb) ... Selecting previously deselected package python27-shlibs. Unpacking python27-shlibs (from .../python27-shlibs_2.7.8-1_darwin-x86_64.deb) ... Setting up python27-shlibs (2.7.8-1) ... Setting up python27 (2.7.8-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/setuptools-tng-py27_5.1-1_darwin-x86_64.deb Selecting previously deselected package setuptools-tng-py27. (Reading database ... 12552 files and directories currently installed.) Unpacking setuptools-tng-py27 (from .../setuptools-tng-py27_5.1-1_darwin-x86_64.deb) ... Setting up setuptools-tng-py27 (5.1-1) ... Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-pysam-py27-0.7.5-1 /sw/build.build dpkg-deb: building package `fink-buildlock-pysam-py27-0.7.5-1' in `/sw/build.build/fink-buildlock-pysam-py27-0.7.5-1_2014.07.30-02.53.12_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-pysam-py27-0.7.5-1_2014.07.30-02.53.12_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-pysam-py27-0.7.5-1. (Reading database ... 12723 files and directories currently installed.) Unpacking fink-buildlock-pysam-py27-0.7.5-1 (from .../fink-buildlock-pysam-py27-0.7.5-1_2014.07.30-02.53.12_darwin-x86_64.deb) ... Setting up fink-buildlock-pysam-py27-0.7.5-1 (2014.07.30-02.53.12) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.rLQUT env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/pysam-0.7.5.tar.gz pysam-0.7.5/ pysam-0.7.5/tabix/ pysam-0.7.5/tabix/bedidx.c pysam-0.7.5/tabix/index.c.pysam.c pysam-0.7.5/tabix/bgzip.c.pysam.c pysam-0.7.5/tabix/index.c pysam-0.7.5/tabix/khash.h pysam-0.7.5/tabix/tabix.h pysam-0.7.5/tabix/kseq.h pysam-0.7.5/tabix/bgzip.c pysam-0.7.5/tabix/knetfile.c.pysam.c pysam-0.7.5/tabix/pysam.h pysam-0.7.5/tabix/bgzf.h pysam-0.7.5/tabix/kstring.c pysam-0.7.5/tabix/knetfile.h pysam-0.7.5/tabix/bgzf.c pysam-0.7.5/tabix/bgzf.c.pysam.c pysam-0.7.5/tabix/bedidx.c.pysam.c pysam-0.7.5/tabix/knetfile.c pysam-0.7.5/tabix/__init__.py pysam-0.7.5/tabix/bam_endian.h pysam-0.7.5/tabix/kstring.c.pysam.c pysam-0.7.5/tabix/ksort.h pysam-0.7.5/tabix/kstring.h pysam-0.7.5/setup.py pysam-0.7.5/pysam.egg-info/ pysam-0.7.5/pysam.egg-info/dependency_links.txt pysam-0.7.5/pysam.egg-info/PKG-INFO pysam-0.7.5/pysam.egg-info/top_level.txt pysam-0.7.5/pysam.egg-info/not-zip-safe pysam-0.7.5/pysam.egg-info/SOURCES.txt pysam-0.7.5/pysam.egg-info/requires.txt pysam-0.7.5/MANIFEST.in pysam-0.7.5/pysam/ pysam-0.7.5/pysam/TabProxies.pyx pysam-0.7.5/pysam/cvcf.c pysam-0.7.5/pysam/TabProxies.c pysam-0.7.5/pysam/pysam_util.c pysam-0.7.5/pysam/version.py pysam-0.7.5/pysam/cvcf.pyx pysam-0.7.5/pysam/include/ pysam-0.7.5/pysam/include/__init__.py pysam-0.7.5/pysam/ctabix.c pysam-0.7.5/pysam/tabix_util.c pysam-0.7.5/pysam/TabProxies.pxd pysam-0.7.5/pysam/cvcf.pxd pysam-0.7.5/pysam/csamtools.pxd pysam-0.7.5/pysam/ctabix.pxd pysam-0.7.5/pysam/pysam_util.h pysam-0.7.5/pysam/ctabix.pyx pysam-0.7.5/pysam/csamtools.c pysam-0.7.5/pysam/tabix_util.h pysam-0.7.5/pysam/Pileup.py pysam-0.7.5/pysam/namedtuple.py pysam-0.7.5/pysam/__init__.py pysam-0.7.5/pysam/csamtools.pyx pysam-0.7.5/setup.cfg pysam-0.7.5/PKG-INFO pysam-0.7.5/THANKS pysam-0.7.5/samtools/ pysam-0.7.5/samtools/bam_sort.c.pysam.c pysam-0.7.5/samtools/bam.h pysam-0.7.5/samtools/win32/ pysam-0.7.5/samtools/win32/zconf.h pysam-0.7.5/samtools/win32/zlib.h pysam-0.7.5/samtools/win32/xcurses.h pysam-0.7.5/samtools/win32/__init__.py pysam-0.7.5/samtools/misc/ pysam-0.7.5/samtools/misc/md5.h pysam-0.7.5/samtools/misc/ace2sam.c.pysam.c pysam-0.7.5/samtools/misc/md5.c.pysam.c pysam-0.7.5/samtools/bam_color.c.pysam.c pysam-0.7.5/samtools/bam_pileup.c.pysam.c pysam-0.7.5/samtools/kaln.c.pysam.c pysam-0.7.5/samtools/bamshuf.c.pysam.c pysam-0.7.5/samtools/kprobaln.c.pysam.c pysam-0.7.5/samtools/faidx.c.pysam.c pysam-0.7.5/samtools/bam_reheader.c.pysam.c pysam-0.7.5/samtools/bam_rmdup.c.pysam.c pysam-0.7.5/samtools/cut_target.c.pysam.c pysam-0.7.5/samtools/bam_import.c.pysam.c pysam-0.7.5/samtools/bam_index.c.pysam.c pysam-0.7.5/samtools/errmod.c.pysam.c pysam-0.7.5/samtools/bedcov.c.pysam.c pysam-0.7.5/samtools/sample.c.pysam.c pysam-0.7.5/samtools/klist.h pysam-0.7.5/samtools/bam_tview.c.pysam.c pysam-0.7.5/samtools/razf.h pysam-0.7.5/samtools/bam_mate.c.pysam.c pysam-0.7.5/samtools/sam_header.h pysam-0.7.5/samtools/sam.c.pysam.c pysam-0.7.5/samtools/kprobaln.h pysam-0.7.5/samtools/bcftools/ pysam-0.7.5/samtools/bcftools/prob1.h pysam-0.7.5/samtools/bcftools/kmin.c.pysam.c pysam-0.7.5/samtools/bcftools/kmin.h pysam-0.7.5/samtools/bcftools/bcfutils.c.pysam.c pysam-0.7.5/samtools/bcftools/kfunc.c.pysam.c pysam-0.7.5/samtools/bcftools/index.c.pysam.c pysam-0.7.5/samtools/bcftools/bcf.c.pysam.c pysam-0.7.5/samtools/bcftools/bcf2qcall.c.pysam.c pysam-0.7.5/samtools/bcftools/prob1.c.pysam.c pysam-0.7.5/samtools/bcftools/fet.c.pysam.c pysam-0.7.5/samtools/bcftools/bcf.h pysam-0.7.5/samtools/bcftools/em.c.pysam.c pysam-0.7.5/samtools/bcftools/vcf.c.pysam.c pysam-0.7.5/samtools/bcftools/call1.c.pysam.c pysam-0.7.5/samtools/bcftools/__init__.py pysam-0.7.5/samtools/bcftools/mut.c.pysam.c pysam-0.7.5/samtools/bam2bcf.h pysam-0.7.5/samtools/errmod.h pysam-0.7.5/samtools/khash.h pysam-0.7.5/samtools/kseq.h pysam-0.7.5/samtools/sample.h pysam-0.7.5/samtools/knetfile.c.pysam.c pysam-0.7.5/samtools/sam_view.c.pysam.c pysam-0.7.5/samtools/pysam.h pysam-0.7.5/samtools/bgzf.h pysam-0.7.5/samtools/bam_tview.h pysam-0.7.5/samtools/bam2bcf_indel.c.pysam.c pysam-0.7.5/samtools/razf.c.pysam.c pysam-0.7.5/samtools/sam.h pysam-0.7.5/samtools/bam_plcmd.c.pysam.c pysam-0.7.5/samtools/bam_lpileup.c.pysam.c pysam-0.7.5/samtools/padding.c.pysam.c pysam-0.7.5/samtools/knetfile.h pysam-0.7.5/samtools/bam_cat.c.pysam.c pysam-0.7.5/samtools/bam2bcf.c.pysam.c pysam-0.7.5/samtools/bam_tview_curses.c.pysam.c pysam-0.7.5/samtools/faidx.h pysam-0.7.5/samtools/bgzf.c.pysam.c pysam-0.7.5/samtools/bam_md.c.pysam.c pysam-0.7.5/samtools/bedidx.c.pysam.c pysam-0.7.5/samtools/bam2depth.c.pysam.c pysam-0.7.5/samtools/__init__.py pysam-0.7.5/samtools/bam_rmdupse.c.pysam.c pysam-0.7.5/samtools/bam_aux.c.pysam.c pysam-0.7.5/samtools/bam.c.pysam.c pysam-0.7.5/samtools/bam_stat.c.pysam.c pysam-0.7.5/samtools/phase.c.pysam.c pysam-0.7.5/samtools/bam_endian.h pysam-0.7.5/samtools/sam_header.c.pysam.c pysam-0.7.5/samtools/kstring.c.pysam.c pysam-0.7.5/samtools/kaln.h pysam-0.7.5/samtools/ksort.h pysam-0.7.5/samtools/kstring.h pysam-0.7.5/samtools/bam_tview_html.c.pysam.c pysam-0.7.5/KNOWN_BUGS pysam-0.7.5/tests/ pysam-0.7.5/tests/ex5.sam pysam-0.7.5/tests/example_btag.sam pysam-0.7.5/tests/ex1.fa pysam-0.7.5/tests/vcf-examples/ pysam-0.7.5/tests/vcf-examples/7.vcf pysam-0.7.5/tests/vcf-examples/3.vcf pysam-0.7.5/tests/vcf-examples/10.vcf pysam-0.7.5/tests/vcf-examples/15.vcf pysam-0.7.5/tests/vcf-examples/23.vcf pysam-0.7.5/tests/vcf-examples/24.vcf pysam-0.7.5/tests/vcf-examples/12.vcf pysam-0.7.5/tests/vcf-examples/21.vcf pysam-0.7.5/tests/vcf-examples/16.vcf pysam-0.7.5/tests/vcf-examples/20.vcf pysam-0.7.5/tests/vcf-examples/9.vcf pysam-0.7.5/tests/vcf-examples/22.vcf pysam-0.7.5/tests/vcf-examples/5.vcf pysam-0.7.5/tests/vcf-examples/6.vcf pysam-0.7.5/tests/vcf-examples/issue85.vcf pysam-0.7.5/tests/vcf-examples/11.vcf pysam-0.7.5/tests/vcf-examples/2.vcf pysam-0.7.5/tests/vcf-examples/8.vcf pysam-0.7.5/tests/vcf-examples/18.vcf pysam-0.7.5/tests/vcf-examples/13.vcf pysam-0.7.5/tests/vcf-examples/4.vcf pysam-0.7.5/tests/example_btag.bam pysam-0.7.5/tests/ex7.sam pysam-0.7.5/tests/example_user_header.sam pysam-0.7.5/tests/ex8.sam pysam-0.7.5/tests/example_unmapped_reads_no_sq.sam pysam-0.7.5/tests/ex4.sam pysam-0.7.5/tests/pysam_test.py pysam-0.7.5/tests/example.bed.gz.tbi pysam-0.7.5/tests/ex10.sam pysam-0.7.5/tests/tabix_test.py pysam-0.7.5/tests/tag_bug.bam pysam-0.7.5/tests/test_unaligned.bam pysam-0.7.5/tests/ex9_nofail.bam pysam-0.7.5/tests/ex1.sam.gz pysam-0.7.5/tests/example.bed.gz pysam-0.7.5/tests/00README.txt pysam-0.7.5/tests/ex9_fail.bam pysam-0.7.5/tests/example.gtf.gz.tbi pysam-0.7.5/tests/ex3.sam pysam-0.7.5/tests/example.gtf.gz pysam-0.7.5/tests/issue100.bam pysam-0.7.5/tests/example.py pysam-0.7.5/tests/example.vcf40 pysam-0.7.5/tests/ex6.sam pysam-0.7.5/tests/example_empty_header.bam pysam-0.7.5/tests/Makefile pysam-0.7.5/tests/segfault_tests.py pysam-0.7.5/doc/ pysam-0.7.5/doc/release.rst pysam-0.7.5/doc/make.bat pysam-0.7.5/doc/faq.rst pysam-0.7.5/doc/usage.rst pysam-0.7.5/doc/developer.rst pysam-0.7.5/doc/api.rst pysam-0.7.5/doc/conf.py pysam-0.7.5/doc/glossary.rst pysam-0.7.5/doc/contents.rst pysam-0.7.5/doc/Makefile pysam-0.7.5/COPYING pysam-0.7.5/pysam.py pysam-0.7.5/INSTALL pysam-0.7.5/distribute_setup.py sudo -u fink-bld [ENV] sh -c /tmp/fink.wPcZt [ -r /sw/fink/dists/stable/main/finkinfo/libs/pythonmods/pysam-py.patch ] sudo -u fink-bld [ENV] sh -c /tmp/fink.IPPE4 patch -p1 < /sw/fink/dists/stable/main/finkinfo/libs/pythonmods/pysam-py.patch patching file setup.py sudo -u fink-bld [ENV] sh -c /tmp/fink.Tr2Pa /sw/bin/python2.7 setup.py build running build running build_py creating build creating build/lib.macosx-10.9-x86_64-2.7 creating build/lib.macosx-10.9-x86_64-2.7/pysam copying pysam/__init__.py -> build/lib.macosx-10.9-x86_64-2.7/pysam copying pysam/namedtuple.py -> build/lib.macosx-10.9-x86_64-2.7/pysam copying pysam/Pileup.py -> build/lib.macosx-10.9-x86_64-2.7/pysam copying pysam/version.py -> build/lib.macosx-10.9-x86_64-2.7/pysam creating build/lib.macosx-10.9-x86_64-2.7/pysam/include copying pysam/include/__init__.py -> build/lib.macosx-10.9-x86_64-2.7/pysam/include creating build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools copying samtools/__init__.py -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools creating build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/bcftools copying samtools/bcftools/__init__.py -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/bcftools creating build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/win32 copying samtools/win32/__init__.py -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/win32 creating build/lib.macosx-10.9-x86_64-2.7/pysam/include/tabix copying tabix/__init__.py -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/tabix copying pysam/csamtools.pxd -> build/lib.macosx-10.9-x86_64-2.7/pysam copying pysam/ctabix.pxd -> build/lib.macosx-10.9-x86_64-2.7/pysam copying pysam/cvcf.pxd -> build/lib.macosx-10.9-x86_64-2.7/pysam copying pysam/TabProxies.pxd -> build/lib.macosx-10.9-x86_64-2.7/pysam copying pysam/pysam_util.h -> build/lib.macosx-10.9-x86_64-2.7/pysam copying pysam/tabix_util.h -> build/lib.macosx-10.9-x86_64-2.7/pysam copying samtools/bam.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools copying samtools/bam2bcf.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools copying samtools/bam_endian.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools copying samtools/bam_tview.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools copying samtools/bgzf.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools copying samtools/errmod.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools copying samtools/faidx.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools copying samtools/kaln.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools copying samtools/khash.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools copying samtools/klist.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools copying samtools/knetfile.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools copying samtools/kprobaln.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools copying samtools/kseq.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools copying samtools/ksort.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools copying samtools/kstring.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools copying samtools/pysam.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools copying samtools/razf.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools copying samtools/sam.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools copying samtools/sam_header.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools copying samtools/sample.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools copying samtools/bcftools/bcf.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/bcftools copying samtools/bcftools/kmin.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/bcftools copying samtools/bcftools/prob1.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/bcftools copying samtools/win32/xcurses.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/win32 copying samtools/win32/zconf.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/win32 copying samtools/win32/zlib.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/win32 copying tabix/bam_endian.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/tabix copying tabix/bgzf.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/tabix copying tabix/khash.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/tabix copying tabix/knetfile.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/tabix copying tabix/kseq.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/tabix copying tabix/ksort.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/tabix copying tabix/kstring.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/tabix copying tabix/pysam.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/tabix copying tabix/tabix.h -> build/lib.macosx-10.9-x86_64-2.7/pysam/include/tabix running build_ext building 'pysam.csamtools' extension creating build/temp.macosx-10.9-x86_64-2.7 creating build/temp.macosx-10.9-x86_64-2.7/pysam creating build/temp.macosx-10.9-x86_64-2.7/samtools creating build/temp.macosx-10.9-x86_64-2.7/samtools/bcftools creating build/temp.macosx-10.9-x86_64-2.7/samtools/misc gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c pysam/csamtools.c -o build/temp.macosx-10.9-x86_64-2.7/pysam/csamtools.o pysam/csamtools.c:10560:167: warning: incompatible pointer types passing 'int (bam1_t *, void *)' to parameter of type 'bam_fetch_f' (aka 'int (*)(const bam1_t *, void *)') [-Wincompatible-pointer-types] __pyx_t_5 = PyInt_FromLong(bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, ((void *)__pyx_v_callback), __pyx_f_5pysam_9csamtools_fetch_callback)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 940; __pyx_clineno = __LINE__; goto __pyx_L1_error;} ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/bam.h:644:103: note: passing argument to parameter 'func' here int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func); ^ pysam/csamtools.c:11025:210: warning: incompatible pointer types passing 'int (bam1_t *, void *)' to parameter of type 'bam_fetch_f' (aka 'int (*)(const bam1_t *, void *)') [-Wincompatible-pointer-types] bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_read->_delegate->core.mtid, __pyx_v_read->_delegate->core.mpos, (__pyx_v_read->_delegate->core.mpos + 1), ((void *)(&__pyx_v_mate_data)), __pyx_f_5pysam_9csamtools_mate_callback); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/bam.h:644:103: note: passing argument to parameter 'func' here int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func); ^ pysam/csamtools.c:11523:140: warning: incompatible pointer types passing 'int (bam1_t *, void *)' to parameter of type 'bam_fetch_f' (aka 'int (*)(const bam1_t *, void *)') [-Wincompatible-pointer-types] bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, ((void *)(&__pyx_v_counter)), __pyx_f_5pysam_9csamtools_count_callback); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/bam.h:644:103: note: passing argument to parameter 'func' here int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func); ^ pysam/csamtools.c:11963:125: warning: incompatible pointer types passing 'int (bam1_t *, void *)' to parameter of type 'bam_fetch_f' (aka 'int (*)(const bam1_t *, void *)') [-Wincompatible-pointer-types] bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, __pyx_v_buf, __pyx_f_5pysam_9csamtools_pileup_fetch_callback); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/bam.h:644:103: note: passing argument to parameter 'func' here int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func); ^ pysam/csamtools.c:18711:7: warning: implicit declaration of function 'bam_prob_realn' is invalid in C99 [-Wimplicit-function-declaration] bam_prob_realn(__pyx_v_b, __pyx_v_d->seq); ^ pysam/csamtools.c:18739:19: warning: implicit declaration of function 'bam_cap_mapQ' is invalid in C99 [-Wimplicit-function-declaration] __pyx_v_q = bam_cap_mapQ(__pyx_v_b, __pyx_v_d->seq, __pyx_v_capQ_thres); ^ pysam/csamtools.c:20277:59: warning: passing 'const bam_pileup1_t **' to parameter of type 'bam_pileup1_t **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers] __pyx_t_2 = __pyx_f_5pysam_9csamtools_makePileupProxy((&__pyx_v_self->__pyx_base.plp), __pyx_v_self->__pyx_base.tid, __pyx_v_self->__pyx_base.pos, __pyx_v_self->__pyx_base.n_plp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1968; __pyx_clineno = __LINE__; goto __pyx_L1_error;} ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/csamtools.c:3683:76: note: passing argument to parameter '__pyx_v_plp' here static PyObject *__pyx_f_5pysam_9csamtools_makePileupProxy(bam_pileup1_t **__pyx_v_plp, int __pyx_v_tid, int __pyx_v_pos, int __pyx_v_n) { ^ pysam/csamtools.c:20530:61: warning: passing 'const bam_pileup1_t **' to parameter of type 'bam_pileup1_t **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers] __pyx_t_2 = __pyx_f_5pysam_9csamtools_makePileupProxy((&__pyx_v_self->__pyx_base.plp), __pyx_v_self->__pyx_base.tid, __pyx_v_self->__pyx_base.pos, __pyx_v_self->__pyx_base.n_plp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1999; __pyx_clineno = __LINE__; goto __pyx_L1_error;} ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/csamtools.c:3683:76: note: passing argument to parameter '__pyx_v_plp' here static PyObject *__pyx_f_5pysam_9csamtools_makePileupProxy(bam_pileup1_t **__pyx_v_plp, int __pyx_v_tid, int __pyx_v_pos, int __pyx_v_n) { ^ pysam/csamtools.c:45221:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ pysam/csamtools.c:993:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) { ^ pysam/csamtools.c:43468:28: warning: unused function '__Pyx_CyFunction_InitDefaults' [-Wunused-function] static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) { ^ pysam/csamtools.c:43968:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ pysam/csamtools.c:43987:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ pysam/csamtools.c:44082:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ 14 warnings generated. gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c pysam/pysam_util.c -o build/temp.macosx-10.9-x86_64-2.7/pysam/pysam_util.o pysam/pysam_util.c:193:8: warning: assigning to 'bam_pileup1_t *' from 'const bam_pileup1_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] *plp = bam_plp_next(buf->iter, tid, pos, n_plp); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/pysam_util.c:419:18: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] if (offset < 0 || offset > b->data_len) ~~~~~~ ^ ~ pysam/pysam_util.c:63:1: warning: unused function 'kh_init_i' [-Wunused-function] KHASH_MAP_INIT_INT(i, bam_binlist_t); ^ samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:168:23: note: expanded from macro 'KHASH_INIT2' SCOPE kh_##name##_t *kh_init_##name() { \ ^ :210:1: note: expanded from here kh_init_i ^ pysam/pysam_util.c:63:1: warning: unused function 'kh_destroy_i' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:171:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_destroy_##name(kh_##name##_t *h) \ ^ :215:1: note: expanded from here kh_destroy_i ^ pysam/pysam_util.c:63:1: warning: unused function 'kh_clear_i' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :218:1: note: expanded from here kh_clear_i ^ pysam/pysam_util.c:63:1: warning: unused function 'kh_put_i' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:260:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \ ^ :227:1: note: expanded from here kh_put_i ^ pysam/pysam_util.c:63:1: warning: unused function 'kh_del_i' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :232:1: note: expanded from here kh_del_i ^ pysam/pysam_util.c:64:1: warning: unused function 'kh_init_s' [-Wunused-function] KHASH_MAP_INIT_STR(s, int) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:168:23: note: expanded from macro 'KHASH_INIT2' SCOPE kh_##name##_t *kh_init_##name() { \ ^ :239:1: note: expanded from here kh_init_s ^ pysam/pysam_util.c:64:1: warning: unused function 'kh_destroy_s' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:171:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_destroy_##name(kh_##name##_t *h) \ ^ :244:1: note: expanded from here kh_destroy_s ^ pysam/pysam_util.c:64:1: warning: unused function 'kh_clear_s' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :247:1: note: expanded from here kh_clear_s ^ pysam/pysam_util.c:64:1: warning: unused function 'kh_put_s' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:260:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \ ^ :256:1: note: expanded from here kh_put_s ^ pysam/pysam_util.c:64:1: warning: unused function 'kh_del_s' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :261:1: note: expanded from here kh_del_s ^ pysam/pysam_util.c:96:19: warning: unused function 'mp_init' [-Wunused-function] static mempool_t *mp_init() ^ pysam/pysam_util.c:102:13: warning: unused function 'mp_destroy' [-Wunused-function] static void mp_destroy(mempool_t *mp) ^ pysam/pysam_util.c:112:25: warning: unused function 'mp_alloc' [-Wunused-function] static inline lbnode_t *mp_alloc(mempool_t *mp) ^ pysam/pysam_util.c:118:20: warning: unused function 'mp_free' [-Wunused-function] static inline void mp_free(mempool_t *mp, lbnode_t *p) ^ pysam/pysam_util.c:128:19: warning: unused function 'resolve_cigar' [-Wunused-function] static inline int resolve_cigar(bam_pileup1_t *p, uint32_t pos) ^ 17 warnings generated. gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bam.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bam.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bam2bcf.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bam2bcf.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bam2bcf_indel.c.pysam.o samtools/bam2bcf_indel.c.pysam.c:34:52: warning: for loop has empty body [-Wempty-body] for (r = p; *r && *r != '\t' && *r != '\n'; ++r); lp = r - p; ^ samtools/bam2bcf_indel.c.pysam.c:34:52: note: put the semicolon on a separate line to silence this warning samtools/bam2bcf_indel.c.pysam.c:35:52: warning: for loop has empty body [-Wempty-body] for (r = q; *r && *r != '\t' && *r != '\n'; ++r); lq = r - q; ^ samtools/bam2bcf_indel.c.pysam.c:35:52: note: put the semicolon on a separate line to silence this warning samtools/bam2bcf_indel.c.pysam.c:11:1: warning: unused function 'kh_clear_rg' [-Wunused-function] KHASH_SET_INIT_STR(rg) ^ samtools/khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR' KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :200:1: note: expanded from here kh_clear_rg ^ samtools/bam2bcf_indel.c.pysam.c:11:1: warning: unused function 'kh_del_rg' [-Wunused-function] samtools/khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR' KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :214:1: note: expanded from here kh_del_rg ^ 4 warnings generated. gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bam2depth.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bam2depth.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bam_aux.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_aux.c.pysam.o samtools/bam_aux.c.pysam.c:7:1: warning: unused function 'kh_clear_s' [-Wunused-function] KHASH_MAP_INIT_STR(s, int) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :200:1: note: expanded from here kh_clear_s ^ samtools/bam_aux.c.pysam.c:7:1: warning: unused function 'kh_del_s' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :214:1: note: expanded from here kh_del_s ^ samtools/bam_aux.c.pysam.c:8:1: warning: unused function 'kh_init_r2l' [-Wunused-function] KHASH_MAP_INIT_STR(r2l, str_p) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:168:23: note: expanded from macro 'KHASH_INIT2' SCOPE kh_##name##_t *kh_init_##name() { \ ^ :221:1: note: expanded from here kh_init_r2l ^ samtools/bam_aux.c.pysam.c:8:1: warning: unused function 'kh_destroy_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:171:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_destroy_##name(kh_##name##_t *h) \ ^ :226:1: note: expanded from here kh_destroy_r2l ^ samtools/bam_aux.c.pysam.c:8:1: warning: unused function 'kh_clear_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :229:1: note: expanded from here kh_clear_r2l ^ samtools/bam_aux.c.pysam.c:8:1: warning: unused function 'kh_get_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:186:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :232:1: note: expanded from here kh_get_r2l ^ samtools/bam_aux.c.pysam.c:8:1: warning: unused function 'kh_put_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:260:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \ ^ :238:1: note: expanded from here kh_put_r2l ^ samtools/bam_aux.c.pysam.c:8:1: warning: unused function 'kh_del_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :243:1: note: expanded from here kh_del_r2l ^ 8 warnings generated. gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bam_cat.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_cat.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bam_color.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_color.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bam_import.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_import.c.pysam.o samtools/bam_import.c.pysam.c:20:1: warning: unused function 'kh_clear_ref' [-Wunused-function] KHASH_MAP_INIT_STR(ref, uint64_t) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :200:1: note: expanded from here kh_clear_ref ^ samtools/bam_import.c.pysam.c:20:1: warning: unused function 'kh_get_ref' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:186:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :203:1: note: expanded from here kh_get_ref ^ samtools/bam_import.c.pysam.c:20:1: warning: unused function 'kh_del_ref' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :214:1: note: expanded from here kh_del_ref ^ 3 warnings generated. gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bam_index.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_index.c.pysam.o samtools/bam_index.c.pysam.c:66:1: warning: unused function 'kh_clear_i' [-Wunused-function] KHASH_MAP_INIT_INT(i, bam_binlist_t) ^ samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :218:1: note: expanded from here kh_clear_i ^ samtools/bam_index.c.pysam.c:66:1: warning: unused function 'kh_del_i' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :232:1: note: expanded from here kh_del_i ^ 2 warnings generated. gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bam_lpileup.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_lpileup.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bam_mate.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_mate.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bam_md.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_md.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bam_pileup.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_pileup.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bam_plcmd.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_plcmd.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bam_reheader.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_reheader.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bam_rmdup.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_rmdup.c.pysam.o samtools/bam_rmdup.c.pysam.c:14:1: warning: unused function 'kh_get_pos' [-Wunused-function] KHASH_MAP_INIT_INT64(pos, bam1_p) ^ samtools/khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64' KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:186:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :232:1: note: expanded from here kh_get_pos ^ samtools/bam_rmdup.c.pysam.c:14:1: warning: unused function 'kh_del_pos' [-Wunused-function] samtools/khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64' KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :243:1: note: expanded from here kh_del_pos ^ samtools/bam_rmdup.c.pysam.c:22:1: warning: unused function 'kh_clear_lib' [-Wunused-function] KHASH_MAP_INIT_STR(lib, lib_aux_t) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :260:1: note: expanded from here kh_clear_lib ^ samtools/bam_rmdup.c.pysam.c:22:1: warning: unused function 'kh_del_lib' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :274:1: note: expanded from here kh_del_lib ^ 4 warnings generated. gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_rmdupse.c.pysam.o samtools/bam_rmdupse.c.pysam.c:20:1: warning: unused function 'kh_clear_best' [-Wunused-function] KHASH_MAP_INIT_INT(best, elem_p) ^ samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :103:1: note: expanded from here kh_clear_best ^ samtools/bam_rmdupse.c.pysam.c:20:1: warning: unused function 'kh_get_best' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:186:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :106:1: note: expanded from here kh_get_best ^ samtools/bam_rmdupse.c.pysam.c:27:1: warning: unused function 'kh_clear_lib' [-Wunused-function] KHASH_MAP_INIT_STR(lib, lib_aux_t) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :134:1: note: expanded from here kh_clear_lib ^ samtools/bam_rmdupse.c.pysam.c:27:1: warning: unused function 'kh_del_lib' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :148:1: note: expanded from here kh_del_lib ^ 4 warnings generated. gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bam_sort.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_sort.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bam_stat.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_stat.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bam_tview.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_tview.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bam_tview_curses.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_tview_curses.c.pysam.o samtools/bam_tview_curses.c.pysam.c:289:2: warning: "No curses library is available; tview with curses is disabled." [-W#warnings] #warning "No curses library is available; tview with curses is disabled." ^ 1 warning generated. gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bam_tview_html.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_tview_html.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bamshuf.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bamshuf.c.pysam.o samtools/bamshuf.c.pysam.c:107:8: warning: unused variable '_l' [-Wunused-variable] int _l = bam_read1(fp, a[j].b); ^ 1 warning generated. gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bedcov.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bedcov.c.pysam.o samtools/bedcov.c.pysam.c:14:1: warning: unused function 'ks_getc' [-Wunused-function] KSTREAM_INIT(gzFile, gzread, 16384) ^ samtools/kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT' __KS_GETC(__read, __bufsize) \ ^ samtools/kseq.h:67:20: note: expanded from macro '__KS_GETC' static inline int ks_getc(kstream_t *ks) \ ^ 1 warning generated. gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bedidx.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bedidx.c.pysam.o samtools/bedidx.c.pysam.c:26:1: warning: unused function 'kh_clear_reg' [-Wunused-function] KHASH_MAP_INIT_STR(reg, bed_reglist_t) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :214:1: note: expanded from here kh_clear_reg ^ samtools/bedidx.c.pysam.c:26:1: warning: unused function 'kh_del_reg' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :228:1: note: expanded from here kh_del_reg ^ 2 warnings generated. gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bgzf.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bgzf.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/cut_target.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/cut_target.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/errmod.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/errmod.c.pysam.o samtools/errmod.c.pysam.c:81:8: warning: self-comparison always evaluates to false [-Wtautological-compare] if (m > m) return -1; ^ 1 warning generated. gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/faidx.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/faidx.c.pysam.o samtools/faidx.c.pysam.c:16:1: warning: unused function 'kh_clear_s' [-Wunused-function] KHASH_MAP_INIT_STR(s, faidx1_t) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :154:1: note: expanded from here kh_clear_s ^ samtools/faidx.c.pysam.c:16:1: warning: unused function 'kh_del_s' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :168:1: note: expanded from here kh_del_s ^ 2 warnings generated. gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/kaln.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/kaln.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/knetfile.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/knetfile.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/kprobaln.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/kprobaln.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/kstring.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/kstring.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/padding.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/padding.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/phase.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/phase.c.pysam.o samtools/phase.c.pysam.c:47:1: warning: unused function 'kh_clear_set64' [-Wunused-function] KHASH_SET_INIT_INT64(set64) ^ samtools/khash.h:502:2: note: expanded from macro 'KHASH_SET_INIT_INT64' KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :49:1: note: expanded from here kh_clear_set64 ^ samtools/phase.c.pysam.c:47:1: warning: unused function 'kh_del_set64' [-Wunused-function] samtools/khash.h:502:2: note: expanded from macro 'KHASH_SET_INIT_INT64' KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :63:1: note: expanded from here kh_del_set64 ^ samtools/phase.c.pysam.c:48:1: warning: unused function 'kh_clear_64' [-Wunused-function] KHASH_MAP_INIT_INT64(64, frag_t) ^ samtools/khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64' KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :78:1: note: expanded from here kh_clear_64 ^ 3 warnings generated. gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/razf.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/razf.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/sam.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/sam.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/sam_header.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/sam_header.c.pysam.o samtools/sam_header.c.pysam.c:11:1: warning: unused function 'kh_clear_str' [-Wunused-function] KHASH_MAP_INIT_STR(str, const char *) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :154:1: note: expanded from here kh_clear_str ^ samtools/sam_header.c.pysam.c:11:1: warning: unused function 'kh_del_str' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :168:1: note: expanded from here kh_del_str ^ 2 warnings generated. gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/sam_view.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/sam_view.c.pysam.o samtools/sam_view.c.pysam.c:14:1: warning: unused function 'kh_clear_rg' [-Wunused-function] KHASH_SET_INIT_STR(rg) ^ samtools/khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR' KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :41:1: note: expanded from here kh_clear_rg ^ samtools/sam_view.c.pysam.c:14:1: warning: unused function 'kh_del_rg' [-Wunused-function] samtools/khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR' KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :55:1: note: expanded from here kh_del_rg ^ 2 warnings generated. gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/sample.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/sample.c.pysam.o samtools/sample.c.pysam.c:7:1: warning: unused function 'kh_clear_sm' [-Wunused-function] KHASH_MAP_INIT_STR(sm, int) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :154:1: note: expanded from here kh_clear_sm ^ samtools/sample.c.pysam.c:7:1: warning: unused function 'kh_del_sm' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :168:1: note: expanded from here kh_del_sm ^ 2 warnings generated. gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bcftools/bcf.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bcftools/bcf.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bcftools/bcf2qcall.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bcftools/bcf2qcall.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bcftools/bcfutils.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bcftools/bcfutils.c.pysam.o samtools/bcftools/bcfutils.c.pysam.c:9:1: warning: unused function 'kh_clear_str2id' [-Wunused-function] KHASH_MAP_INIT_STR(str2id, int) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :47:1: note: expanded from here kh_clear_str2id ^ samtools/bcftools/bcfutils.c.pysam.c:9:1: warning: unused function 'kh_del_str2id' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :61:1: note: expanded from here kh_del_str2id ^ 2 warnings generated. gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bcftools/call1.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bcftools/call1.c.pysam.o samtools/bcftools/call1.c.pysam.c:19:1: warning: unused function 'ks_getc' [-Wunused-function] KSTREAM_INIT(gzFile, gzread, 16384) ^ samtools/kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT' __KS_GETC(__read, __bufsize) \ ^ samtools/kseq.h:67:20: note: expanded from macro '__KS_GETC' static inline int ks_getc(kstream_t *ks) \ ^ 1 warning generated. gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bcftools/em.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bcftools/em.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bcftools/fet.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bcftools/fet.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bcftools/index.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bcftools/index.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bcftools/kfunc.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bcftools/kfunc.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bcftools/kmin.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bcftools/kmin.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bcftools/mut.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bcftools/mut.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bcftools/prob1.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bcftools/prob1.c.pysam.o samtools/bcftools/prob1.c.pysam.c:15:1: warning: unused function 'ks_getc' [-Wunused-function] KSTREAM_INIT(gzFile, gzread, 16384) ^ samtools/kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT' __KS_GETC(__read, __bufsize) \ ^ samtools/kseq.h:67:20: note: expanded from macro '__KS_GETC' static inline int ks_getc(kstream_t *ks) \ ^ 1 warning generated. gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/bcftools/vcf.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/bcftools/vcf.c.pysam.o samtools/bcftools/vcf.c.pysam.c:245:15: warning: explicitly assigning a variable of type 'int' to itself [-Wself-assign] endblock: i = i; ~ ^ ~ samtools/bcftools/vcf.c.pysam.c:10:1: warning: unused function 'ks_getc' [-Wunused-function] KSTREAM_INIT(gzFile, gzread, 4096) ^ samtools/kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT' __KS_GETC(__read, __bufsize) \ ^ samtools/kseq.h:67:20: note: expanded from macro '__KS_GETC' static inline int ks_getc(kstream_t *ks) \ ^ 2 warnings generated. gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/misc/ace2sam.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/misc/ace2sam.c.pysam.o samtools/misc/ace2sam.c.pysam.c:35:1: warning: unused function 'ks_getc' [-Wunused-function] KSTREAM_INIT(gzFile, gzread, 16384) ^ samtools/kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT' __KS_GETC(__read, __bufsize) \ ^ samtools/kseq.h:67:20: note: expanded from macro '__KS_GETC' static inline int ks_getc(kstream_t *ks) \ ^ 1 warning generated. gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/sw/include/python2.7 -c samtools/misc/md5.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/samtools/misc/md5.c.pysam.o samtools/misc/md5.c.pysam.c:157:27: warning: 'memset' call operates on objects of type 'struct MD5Context' while the size is based on a different type 'struct MD5Context *' [-Wsizeof-pointer-memaccess] memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */ ~~~ ^~~ samtools/misc/md5.c.pysam.c:157:27: note: did you mean to dereference the argument to 'sizeof' (and multiply it by the number of elements)? memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */ ^~~ 1 warning generated. gcc -L/sw/lib -bundle -L/sw/lib/python2.7/config -lpython2.7 -L/sw/lib -L/sw/lib -I/sw/include build/temp.macosx-10.9-x86_64-2.7/pysam/csamtools.o build/temp.macosx-10.9-x86_64-2.7/pysam/pysam_util.o build/temp.macosx-10.9-x86_64-2.7/samtools/bam.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bam2bcf.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bam2bcf_indel.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bam2depth.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_aux.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_cat.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_color.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_import.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_index.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_lpileup.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_mate.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_md.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_pileup.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_plcmd.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_reheader.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_rmdup.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_rmdupse.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_sort.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_stat.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_tview.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_tview_curses.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bam_tview_html.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bamshuf.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bedcov.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bedidx.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bgzf.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/cut_target.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/errmod.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/faidx.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/kaln.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/knetfile.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/kprobaln.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/kstring.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/padding.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/phase.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/razf.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/sam.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/sam_header.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/sam_view.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/sample.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bcftools/bcf.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bcftools/bcf2qcall.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bcftools/bcfutils.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bcftools/call1.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bcftools/em.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bcftools/fet.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bcftools/index.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bcftools/kfunc.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bcftools/kmin.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bcftools/mut.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bcftools/prob1.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/bcftools/vcf.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/misc/ace2sam.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/samtools/misc/md5.c.pysam.o -L/sw/lib -lz -o build/lib.macosx-10.9-x86_64-2.7/pysam/csamtools.so building 'pysam.ctabix' extension creating build/temp.macosx-10.9-x86_64-2.7/tabix gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Itabix -Ipysam -I/sw/include/python2.7 -c pysam/ctabix.c -o build/temp.macosx-10.9-x86_64-2.7/pysam/ctabix.o pysam/ctabix.c:4043:21: warning: assigning to 'char **' from 'const char **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers] __pyx_v_sequences = ti_seqname(__pyx_v_self->tabixfile->idx, (&__pyx_v_nsequences)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/ctabix.c:4544:15: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] __pyx_v_s = ti_read(__pyx_v_self->tabixfile, __pyx_v_self->iterator, (&__pyx_v_len)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/ctabix.c:4896:13: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] __pyx_v_s = ti_read(__pyx_v_self->tabixfile, __pyx_v_self->iterator, (&__pyx_v_len)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/ctabix.c:5819:15: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] __pyx_v_s = ti_read(__pyx_v_self->tabixfile, __pyx_v_self->iterator, (&__pyx_v_len)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/ctabix.c:14078:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ pysam/ctabix.c:14099:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ pysam/ctabix.c:12204:27: warning: unused function '__Pyx_ErrFetch' [-Wunused-function] static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { ^ pysam/ctabix.c:783:32: warning: unused function '__Pyx_GetItemInt_List_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) { ^ pysam/ctabix.c:803:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) { ^ pysam/ctabix.c:13224:28: warning: unused function '__Pyx_CyFunction_InitDefaults' [-Wunused-function] static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) { ^ pysam/ctabix.c:13233:27: warning: unused function '__Pyx_CyFunction_SetDefaultsTuple' [-Wunused-function] static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) { ^ pysam/ctabix.c:13353:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ pysam/ctabix.c:13372:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ pysam/ctabix.c:13467:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ pysam/ctabix.c:13591:35: warning: function '__Pyx_PyInt_AsLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { ^ pysam/ctabix.c:1512:18: warning: unused function '__pyx_f_5pysam_6ctabix_from_string_and_size' [-Wunused-function] static PyObject *__pyx_f_5pysam_6ctabix_from_string_and_size(char *__pyx_v_s, size_t __pyx_v_length) { ^ pysam/ctabix.c:1866:32: warning: unused function '__pyx_f_5pysam_6ctabix__force_cmdline_bytes' [-Wunused-function] static CYTHON_INLINE PyObject *__pyx_f_5pysam_6ctabix__force_cmdline_bytes(PyObject *__pyx_v_s) { ^ pysam/ctabix.c:1982:18: warning: unused function '__pyx_f_5pysam_6ctabix__force_str' [-Wunused-function] static PyObject *__pyx_f_5pysam_6ctabix__force_str(PyObject *__pyx_v_s) { ^ 18 warnings generated. gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Itabix -Ipysam -I/sw/include/python2.7 -c pysam/tabix_util.c -o build/temp.macosx-10.9-x86_64-2.7/pysam/tabix_util.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Itabix -Ipysam -I/sw/include/python2.7 -c tabix/bedidx.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/tabix/bedidx.c.pysam.o tabix/bedidx.c.pysam.c:22:1: warning: unused function 'kh_clear_reg' [-Wunused-function] KHASH_MAP_INIT_STR(reg, bed_reglist_t) ^ tabix/khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ tabix/khash.h:140:21: note: expanded from macro 'KHASH_INIT' static inline void kh_clear_##name(kh_##name##_t *h) \ ^ :212:1: note: expanded from here kh_clear_reg ^ tabix/bedidx.c.pysam.c:22:1: warning: unused function 'kh_del_reg' [-Wunused-function] tabix/khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ tabix/khash.h:259:21: note: expanded from macro 'KHASH_INIT' static inline void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :226:1: note: expanded from here kh_del_reg ^ 2 warnings generated. gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Itabix -Ipysam -I/sw/include/python2.7 -c tabix/bgzf.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/tabix/bgzf.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Itabix -Ipysam -I/sw/include/python2.7 -c tabix/bgzip.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/tabix/bgzip.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Itabix -Ipysam -I/sw/include/python2.7 -c tabix/index.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/tabix/index.c.pysam.o tabix/index.c.pysam.c:36:1: warning: unused function 'kh_clear_i' [-Wunused-function] KHASH_MAP_INIT_INT(i, ti_binlist_t) ^ tabix/khash.h:453:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, uint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ tabix/khash.h:140:21: note: expanded from macro 'KHASH_INIT' static inline void kh_clear_##name(kh_##name##_t *h) \ ^ :25:1: note: expanded from here kh_clear_i ^ tabix/index.c.pysam.c:36:1: warning: unused function 'kh_del_i' [-Wunused-function] tabix/khash.h:453:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, uint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ tabix/khash.h:259:21: note: expanded from macro 'KHASH_INIT' static inline void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :39:1: note: expanded from here kh_del_i ^ tabix/index.c.pysam.c:37:1: warning: unused function 'kh_clear_s' [-Wunused-function] KHASH_MAP_INIT_STR(s, int) ^ tabix/khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ tabix/khash.h:140:21: note: expanded from macro 'KHASH_INIT' static inline void kh_clear_##name(kh_##name##_t *h) \ ^ :54:1: note: expanded from here kh_clear_s ^ tabix/index.c.pysam.c:37:1: warning: unused function 'kh_del_s' [-Wunused-function] tabix/khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ tabix/khash.h:259:21: note: expanded from macro 'KHASH_INIT' static inline void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :68:1: note: expanded from here kh_del_s ^ 4 warnings generated. gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Itabix -Ipysam -I/sw/include/python2.7 -c tabix/knetfile.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/tabix/knetfile.c.pysam.o gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Itabix -Ipysam -I/sw/include/python2.7 -c tabix/kstring.c.pysam.c -o build/temp.macosx-10.9-x86_64-2.7/tabix/kstring.c.pysam.o gcc -L/sw/lib -bundle -L/sw/lib/python2.7/config -lpython2.7 -L/sw/lib -L/sw/lib -I/sw/include build/temp.macosx-10.9-x86_64-2.7/pysam/ctabix.o build/temp.macosx-10.9-x86_64-2.7/pysam/tabix_util.o build/temp.macosx-10.9-x86_64-2.7/tabix/bedidx.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/tabix/bgzf.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/tabix/bgzip.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/tabix/index.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/tabix/knetfile.c.pysam.o build/temp.macosx-10.9-x86_64-2.7/tabix/kstring.c.pysam.o -L/sw/lib -lz -o build/lib.macosx-10.9-x86_64-2.7/pysam/ctabix.so building 'pysam.TabProxies' extension gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -I/sw/include/python2.7 -c pysam/TabProxies.c -o build/temp.macosx-10.9-x86_64-2.7/pysam/TabProxies.o pysam/TabProxies.c:2797:33: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] __pyx_t_4 = (__pyx_v_nbytes < 0); ~~~~~~~~~~~~~~ ^ ~ pysam/TabProxies.c:12655:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ pysam/TabProxies.c:12663:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ pysam/TabProxies.c:12676:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ pysam/TabProxies.c:635:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) { ^ pysam/TabProxies.c:11930:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ pysam/TabProxies.c:11949:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ pysam/TabProxies.c:12044:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ pysam/TabProxies.c:12168:35: warning: function '__Pyx_PyInt_AsLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { ^ pysam/TabProxies.c:1180:18: warning: unused function '__pyx_f_5pysam_10TabProxies_from_string_and_size' [-Wunused-function] static PyObject *__pyx_f_5pysam_10TabProxies_from_string_and_size(char *__pyx_v_s, size_t __pyx_v_length) { ^ pysam/TabProxies.c:1253:18: warning: unused function '__pyx_f_5pysam_10TabProxies__my_encodeFilename' [-Wunused-function] static PyObject *__pyx_f_5pysam_10TabProxies__my_encodeFilename(PyObject *__pyx_v_filename) { ^ pysam/TabProxies.c:1534:32: warning: unused function '__pyx_f_5pysam_10TabProxies__force_cmdline_bytes' [-Wunused-function] static CYTHON_INLINE PyObject *__pyx_f_5pysam_10TabProxies__force_cmdline_bytes(PyObject *__pyx_v_s) { ^ pysam/TabProxies.c:1577:18: warning: unused function '__pyx_f_5pysam_10TabProxies__charptr_to_str' [-Wunused-function] static PyObject *__pyx_f_5pysam_10TabProxies__charptr_to_str(char *__pyx_v_s) { ^ pysam/TabProxies.c:1775:14: warning: unused function '__pyx_f_5pysam_10TabProxies_nextItem' [-Wunused-function] static char *__pyx_f_5pysam_10TabProxies_nextItem(char *__pyx_v_buffer) { ^ 14 warnings generated. gcc -L/sw/lib -bundle -L/sw/lib/python2.7/config -lpython2.7 -L/sw/lib -L/sw/lib -I/sw/include build/temp.macosx-10.9-x86_64-2.7/pysam/TabProxies.o -L/sw/lib -lz -o build/lib.macosx-10.9-x86_64-2.7/pysam/TabProxies.so building 'pysam.cvcf' extension gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -I/sw/include -Itabix -I/sw/include/python2.7 -c pysam/cvcf.c -o build/temp.macosx-10.9-x86_64-2.7/pysam/cvcf.o pysam/cvcf.c:29842:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ pysam/cvcf.c:29855:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ pysam/cvcf.c:910:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) { ^ pysam/cvcf.c:28532:36: warning: unused function '__Pyx_PyInt_AsUnsignedChar' [-Wunused-function] static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { ^ pysam/cvcf.c:28551:37: warning: unused function '__Pyx_PyInt_AsUnsignedShort' [-Wunused-function] static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { ^ pysam/cvcf.c:28570:35: warning: unused function '__Pyx_PyInt_AsUnsignedInt' [-Wunused-function] static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { ^ pysam/cvcf.c:28589:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ pysam/cvcf.c:28608:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ pysam/cvcf.c:28646:34: warning: unused function '__Pyx_PyInt_AsSignedChar' [-Wunused-function] static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { ^ pysam/cvcf.c:28665:35: warning: unused function '__Pyx_PyInt_AsSignedShort' [-Wunused-function] static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { ^ pysam/cvcf.c:28684:33: warning: unused function '__Pyx_PyInt_AsSignedInt' [-Wunused-function] static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { ^ pysam/cvcf.c:28703:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ pysam/cvcf.c:28827:35: warning: function '__Pyx_PyInt_AsLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { ^ pysam/cvcf.c:28897:42: warning: function '__Pyx_PyInt_AsSignedLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { ^ 14 warnings generated. gcc -L/sw/lib -bundle -L/sw/lib/python2.7/config -lpython2.7 -L/sw/lib -L/sw/lib -I/sw/include build/temp.macosx-10.9-x86_64-2.7/pysam/cvcf.o -L/sw/lib -lz -o build/lib.macosx-10.9-x86_64-2.7/pysam/cvcf.so /bin/rm -rf /sw/build.build/root-pysam-py27-0.7.5-1 /bin/mkdir -p /sw/build.build/root-pysam-py27-0.7.5-1/sw /bin/mkdir -p /sw/build.build/root-pysam-py27-0.7.5-1/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-pysam-py27-0.7.5-1 sudo -u fink-bld [ENV] sh -c /tmp/fink.KZAuY /sw/bin/python2.7 setup.py install --root /sw/build.build/root-pysam-py27-0.7.5-1 running install running build running build_py running build_ext running install_lib creating /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib creating /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7 creating /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages creating /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam copying build/lib.macosx-10.9-x86_64-2.7/pysam/__init__.py -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam copying build/lib.macosx-10.9-x86_64-2.7/pysam/csamtools.pxd -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam copying build/lib.macosx-10.9-x86_64-2.7/pysam/csamtools.so -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam copying build/lib.macosx-10.9-x86_64-2.7/pysam/ctabix.pxd -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam copying build/lib.macosx-10.9-x86_64-2.7/pysam/ctabix.so -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam copying build/lib.macosx-10.9-x86_64-2.7/pysam/cvcf.pxd -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam copying build/lib.macosx-10.9-x86_64-2.7/pysam/cvcf.so -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam creating /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/__init__.py -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include creating /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/__init__.py -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/bam.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/bam2bcf.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/bam_endian.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/bam_tview.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools creating /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools/bcftools copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/bcftools/__init__.py -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools/bcftools copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/bcftools/bcf.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools/bcftools copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/bcftools/kmin.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools/bcftools copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/bcftools/prob1.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools/bcftools copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/bgzf.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/errmod.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/faidx.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/kaln.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/khash.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/klist.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/knetfile.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/kprobaln.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/kseq.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/ksort.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/kstring.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/pysam.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/razf.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/sam.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/sam_header.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/sample.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools creating /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools/win32 copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/win32/__init__.py -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools/win32 copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/win32/xcurses.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools/win32 copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/win32/zconf.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools/win32 copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/samtools/win32/zlib.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools/win32 creating /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/tabix copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/tabix/__init__.py -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/tabix copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/tabix/bam_endian.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/tabix copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/tabix/bgzf.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/tabix copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/tabix/khash.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/tabix copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/tabix/knetfile.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/tabix copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/tabix/kseq.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/tabix copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/tabix/ksort.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/tabix copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/tabix/kstring.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/tabix copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/tabix/pysam.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/tabix copying build/lib.macosx-10.9-x86_64-2.7/pysam/include/tabix/tabix.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/tabix copying build/lib.macosx-10.9-x86_64-2.7/pysam/namedtuple.py -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam copying build/lib.macosx-10.9-x86_64-2.7/pysam/Pileup.py -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam copying build/lib.macosx-10.9-x86_64-2.7/pysam/pysam_util.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam copying build/lib.macosx-10.9-x86_64-2.7/pysam/tabix_util.h -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam copying build/lib.macosx-10.9-x86_64-2.7/pysam/TabProxies.pxd -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam copying build/lib.macosx-10.9-x86_64-2.7/pysam/TabProxies.so -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam copying build/lib.macosx-10.9-x86_64-2.7/pysam/version.py -> /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam byte-compiling /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/__init__.py to __init__.pyc byte-compiling /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/__init__.py to __init__.pyc byte-compiling /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools/__init__.py to __init__.pyc byte-compiling /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools/bcftools/__init__.py to __init__.pyc byte-compiling /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/samtools/win32/__init__.py to __init__.pyc byte-compiling /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/include/tabix/__init__.py to __init__.pyc byte-compiling /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/namedtuple.py to namedtuple.pyc byte-compiling /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/Pileup.py to Pileup.pyc byte-compiling /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam/version.py to version.pyc running install_egg_info running egg_info writing requirements to pysam.egg-info/requires.txt 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' writing manifest file 'pysam.egg-info/SOURCES.txt' Copying pysam.egg-info to /sw/build.build/root-pysam-py27-0.7.5-1/sw/lib/python2.7/site-packages/pysam-0.7.5-py2.7.egg-info running install_scripts sudo -u fink-bld [ENV] sh -c /tmp/fink.bV9vd /usr/bin/install -d -m 700 /sw/build.build/root-pysam-py27-0.7.5-1/sw/share/doc/pysam-py27 /bin/cp -r COPYING /sw/build.build/root-pysam-py27-0.7.5-1/sw/share/doc/pysam-py27/ /bin/cp -r INSTALL /sw/build.build/root-pysam-py27-0.7.5-1/sw/share/doc/pysam-py27/ /bin/cp -r THANKS /sw/build.build/root-pysam-py27-0.7.5-1/sw/share/doc/pysam-py27/ /bin/chmod -R go=u-w /sw/build.build/root-pysam-py27-0.7.5-1/sw/share/doc/pysam-py27 /bin/rm -f /sw/build.build/root-pysam-py27-0.7.5-1/sw/info/dir /sw/build.build/root-pysam-py27-0.7.5-1/sw/info/dir.old /sw/build.build/root-pysam-py27-0.7.5-1/sw/share/info/dir /sw/build.build/root-pysam-py27-0.7.5-1/sw/share/info/dir.old Reverting ownership of install dir to root Writing control file... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-pysam-py27-0.7.5-1 /sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/pythonmods dpkg-deb: building package `pysam-py27' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/pythonmods/pysam-py27_0.7.5-1_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-pysam-py27-0.7.5-1 (Reading database ... 12724 files and directories currently installed.) Removing fink-buildlock-pysam-py27-0.7.5-1 ...