printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild lofreq 2>&1 The package 'lofreq' will be built without being installed. Reading build dependency for lofreq-0.6.1-1... Reading dependency for lofreq-0.6.1-1... Reading build conflict for lofreq-0.6.1-1... 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 '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 'libncursesw5-shlibs' will be installed. Reading dependency for libncursesw5-shlibs-5.9-20110507-1... Reading runtime dependency for libncursesw5-shlibs-5.9-20110507-1... 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 'readline6-shlibs' will be installed. Reading dependency for readline6-shlibs-6.3.6-1... Reading runtime dependency for readline6-shlibs-6.3.6-1... 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 'libjpeg9-shlibs' will be installed. Reading dependency for libjpeg9-shlibs-9a-1... Reading runtime dependency for libjpeg9-shlibs-9a-1... 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 'freetype219-shlibs' will be installed. Reading dependency for freetype219-shlibs-2.4.12-1... Reading runtime dependency for freetype219-shlibs-2.4.12-1... 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: lofreq The following 18 additional packages will be installed: blt-shlibs db53-aes-shlibs expat1-shlibs fontconfig-config fontconfig2-shlibs freetype219-shlibs gdbm3-shlibs libffi6-shlibs libjpeg9-shlibs libncursesw5-shlibs openssl100-shlibs python27 python27-shlibs readline6-shlibs 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/lofreq-0.6.1.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 28 513k 28 148k 0 0 149k 0 0:00:03 --:--:-- 0:00:03 149k 100 513k 100 513k 0 0 338k 0 0:00:01 0:00:01 --:--:-- 338k 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 ... 4740 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 ... 4750 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/graphics/freetype219-shlibs_2.4.12-1_darwin-x86_64.deb Selecting previously deselected package freetype219-shlibs. (Reading database ... 4755 files and directories currently installed.) Unpacking freetype219-shlibs (from .../freetype219-shlibs_2.4.12-1_darwin-x86_64.deb) ... Setting up freetype219-shlibs (2.4.12-1) ... 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 ... 4766 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 ... 4774 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/graphics/libjpeg9-shlibs_9a-1_darwin-x86_64.deb Selecting previously deselected package libjpeg9-shlibs. (Reading database ... 4775 files and directories currently installed.) Unpacking libjpeg9-shlibs (from .../libjpeg9-shlibs_9a-1_darwin-x86_64.deb) ... Setting up libjpeg9-shlibs (9a-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/base/libncursesw5-shlibs_5.9-20110507-1_darwin-x86_64.deb Selecting previously deselected package libncursesw5-shlibs. (Reading database ... 4778 files and directories currently installed.) Unpacking libncursesw5-shlibs (from .../libncursesw5-shlibs_5.9-20110507-1_darwin-x86_64.deb) ... Setting up libncursesw5-shlibs (5.9-20110507-1) ... 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 ... 4789 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/dists/stable/main/binary-darwin-x86_64/libs/readline6-shlibs_6.3.6-1_darwin-x86_64.deb Selecting previously deselected package readline6-shlibs. (Reading database ... 4810 files and directories currently installed.) Unpacking readline6-shlibs (from .../readline6-shlibs_6.3.6-1_darwin-x86_64.deb) ... Setting up readline6-shlibs (6.3.6-1) ... 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 ... 4821 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/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 ... 4825 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/x11/xft2-shlibs_2.2.0-3_darwin-x86_64.deb Selecting previously deselected package xft2-shlibs. (Reading database ... 4910 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 ... 4919 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 ... 5395 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 ... 5401 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) ... Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-lofreq-0.6.1-1 /sw/build.build dpkg-deb: building package `fink-buildlock-lofreq-0.6.1-1' in `/sw/build.build/fink-buildlock-lofreq-0.6.1-1_2014.08.05-10.57.58_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-lofreq-0.6.1-1_2014.08.05-10.57.58_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-lofreq-0.6.1-1. (Reading database ... 12612 files and directories currently installed.) Unpacking fink-buildlock-lofreq-0.6.1-1 (from .../fink-buildlock-lofreq-0.6.1-1_2014.08.05-10.57.58_darwin-x86_64.deb) ... Setting up fink-buildlock-lofreq-0.6.1-1 (2014.08.05-10.57.58) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.mwjdn env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/lofreq-0.6.1.tar.gz lofreq-0.6.1/ lofreq-0.6.1/README lofreq-0.6.1/configure.ac lofreq-0.6.1/aclocal.m4 lofreq-0.6.1/Makefile.am lofreq-0.6.1/Makefile.in lofreq-0.6.1/configure lofreq-0.6.1/AUTHORS lofreq-0.6.1/COPYING lofreq-0.6.1/ChangeLog lofreq-0.6.1/INSTALL lofreq-0.6.1/NEWS lofreq-0.6.1/config.guess lofreq-0.6.1/config.sub lofreq-0.6.1/depcomp lofreq-0.6.1/install-sh lofreq-0.6.1/ltmain.sh lofreq-0.6.1/missing lofreq-0.6.1/src/ lofreq-0.6.1/src/cdflib90/ lofreq-0.6.1/src/cdflib90/Makefile.am lofreq-0.6.1/src/cdflib90/Makefile.in lofreq-0.6.1/src/cdflib90/cdflib.h lofreq-0.6.1/src/cdflib90/dcdflib.c lofreq-0.6.1/src/cdflib90/ipmpar.c lofreq-0.6.1/src/cdflib90/readme lofreq-0.6.1/src/libbam/ lofreq-0.6.1/src/libbam/Makefile.am lofreq-0.6.1/src/libbam/Makefile.in lofreq-0.6.1/src/libbam/AUTHORS lofreq-0.6.1/src/libbam/COPYING lofreq-0.6.1/src/libbam/bgzf.c lofreq-0.6.1/src/libbam/kstring.c lofreq-0.6.1/src/libbam/bam_aux.c lofreq-0.6.1/src/libbam/bam.c lofreq-0.6.1/src/libbam/bam_import.c lofreq-0.6.1/src/libbam/sam.c lofreq-0.6.1/src/libbam/bam_index.c lofreq-0.6.1/src/libbam/bam_pileup.c lofreq-0.6.1/src/libbam/bam_lpileup.c lofreq-0.6.1/src/libbam/bam_md.c lofreq-0.6.1/src/libbam/razf.c lofreq-0.6.1/src/libbam/faidx.c lofreq-0.6.1/src/libbam/bedidx.c lofreq-0.6.1/src/libbam/knetfile.c lofreq-0.6.1/src/libbam/sam_header.c lofreq-0.6.1/src/libbam/kprobaln.c lofreq-0.6.1/src/libbam/bam.h lofreq-0.6.1/src/libbam/bam_endian.h lofreq-0.6.1/src/libbam/bgzf.h lofreq-0.6.1/src/libbam/faidx.h lofreq-0.6.1/src/libbam/kaln.h lofreq-0.6.1/src/libbam/khash.h lofreq-0.6.1/src/libbam/knetfile.h lofreq-0.6.1/src/libbam/kprobaln.h lofreq-0.6.1/src/libbam/kseq.h lofreq-0.6.1/src/libbam/ksort.h lofreq-0.6.1/src/libbam/kstring.h lofreq-0.6.1/src/libbam/razf.h lofreq-0.6.1/src/libbam/sam.h lofreq-0.6.1/src/libbam/sam_header.h lofreq-0.6.1/src/helper_scripts/ lofreq-0.6.1/src/helper_scripts/base_qual_calib_wrapper.sh lofreq-0.6.1/src/helper_scripts/bwa_unique.sh lofreq-0.6.1/src/helper_scripts/Makefile.am lofreq-0.6.1/src/helper_scripts/Makefile.in lofreq-0.6.1/src/lofreq_core/ lofreq-0.6.1/src/lofreq_core/Makefile.am lofreq-0.6.1/src/lofreq_core/Makefile.in lofreq-0.6.1/src/lofreq_core/bam2depth.c lofreq-0.6.1/src/lofreq_core/binom.c lofreq-0.6.1/src/lofreq_core/fet.c lofreq-0.6.1/src/lofreq_core/sam_view.c lofreq-0.6.1/src/lofreq_core/snpcaller.c lofreq-0.6.1/src/lofreq_core/utils.c lofreq-0.6.1/src/lofreq_core/bam2depth.h lofreq-0.6.1/src/lofreq_core/binom.h lofreq-0.6.1/src/lofreq_core/fet.h lofreq-0.6.1/src/lofreq_core/sam_view.h lofreq-0.6.1/src/lofreq_core/snpcaller.h lofreq-0.6.1/src/lofreq_core/utils.h lofreq-0.6.1/src/lofreq_core/fet.c.AUTHORS lofreq-0.6.1/src/lofreq_core/fet.c.COPYING lofreq-0.6.1/src/lofreq_samtools/ lofreq-0.6.1/src/lofreq_samtools/Makefile.am lofreq-0.6.1/src/lofreq_samtools/Makefile.in lofreq-0.6.1/src/lofreq_samtools/bam_plcmd.c lofreq-0.6.1/src/lofreq_python/ lofreq-0.6.1/src/lofreq_python/lofreq/ lofreq-0.6.1/src/lofreq_python/lofreq/__init__.py lofreq-0.6.1/src/lofreq_python/lofreq/conf.py lofreq-0.6.1/src/lofreq_python/lofreq/em.py lofreq-0.6.1/src/lofreq_python/lofreq/fasta_parser.py lofreq-0.6.1/src/lofreq_python/lofreq/multiple_testing.py lofreq-0.6.1/src/lofreq_python/lofreq/posmap.py lofreq-0.6.1/src/lofreq_python/lofreq/qual.py lofreq-0.6.1/src/lofreq_python/lofreq/sam.py lofreq-0.6.1/src/lofreq_python/lofreq/simple_vcf.py lofreq-0.6.1/src/lofreq_python/lofreq/snp.py lofreq-0.6.1/src/lofreq_python/lofreq/utils.py lofreq-0.6.1/src/lofreq_python/lofreq_ext/ lofreq-0.6.1/src/lofreq_python/lofreq_ext/lofreq_ext.c lofreq-0.6.1/src/lofreq_python/scripts/ lofreq-0.6.1/src/lofreq_python/scripts/lofreq_alnoffset.py lofreq-0.6.1/src/lofreq_python/scripts/lofreq_bonf.py lofreq-0.6.1/src/lofreq_python/scripts/lofreq_diff.py lofreq-0.6.1/src/lofreq_python/scripts/lofreq_filter.py lofreq-0.6.1/src/lofreq_python/scripts/lofreq_pileup_summary.py lofreq-0.6.1/src/lofreq_python/scripts/lofreq_regionbed.py lofreq-0.6.1/src/lofreq_python/scripts/lofreq_snpcaller.py lofreq-0.6.1/src/lofreq_python/scripts/lofreq_uniq.py lofreq-0.6.1/src/lofreq_python/scripts/lofreq_uniq_pipeline.py lofreq-0.6.1/src/lofreq_python/scripts/lofreq_varpos_to_vcf.py lofreq-0.6.1/src/lofreq_python/scripts/lofreq_version.py lofreq-0.6.1/src/lofreq_python/utils/ lofreq-0.6.1/src/lofreq_python/utils/lofreq_ign_pos.py lofreq-0.6.1/src/lofreq_python/utils/lofreq_others.py lofreq-0.6.1/src/lofreq_python/Makefile.am lofreq-0.6.1/src/lofreq_python/Makefile.in lofreq-0.6.1/src/lofreq_python/setup_conf.py.in lofreq-0.6.1/src/lofreq_python/setup.py sudo -u fink-bld [ENV] sh -c /tmp/fink.Tbqka perl -pi -e 's|prefix '\''\$\(prefix\)'\''|$& --root /sw/build.build/root-lofreq-0.6.1-1|g' src/lofreq_python/Makefile.in sudo -u fink-bld [ENV] sh -c /tmp/fink.Vznnf /tmp/fink.HxVDd #!/bin/sh -ev export PYTHON=/sw/bin/python2.7 ./configure --prefix=/sw configure: configuring Lofreq (version 0.6.1) for your system... checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... ./install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking for style of include used by make... GNU checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking dependency style of gcc... gcc3 checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking minix/config.h usability... no checking minix/config.h presence... no checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking build system type... x86_64-apple-darwin13.3.0 checking host system type... x86_64-apple-darwin13.3.0 checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /usr/bin/sed checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld checking if the linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) is GNU ld... no checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm checking the name lister (/usr/bin/nm) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 196608 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking for /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld option to reload object files... -r checking for objdump... no checking how to recognize dependent libraries... pass_all checking for ar... ar checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm output from gcc object... ok checking for dsymutil... dsymutil checking for nmedit... nmedit checking for lipo... lipo checking for otool... otool checking for otool64... no checking for -single_module linker flag... yes checking for -exported_symbols_list linker flag... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... yes checking for gcc option to produce PIC... -fno-common -DPIC checking if gcc PIC flag -fno-common -DPIC works... yes checking if gcc static flag -static works... no checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin13.3.0 dyld checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking for a BSD-compatible install... /usr/bin/install -c checking for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking dependency style of gcc... (cached) gcc3 checking how to run the C preprocessor... gcc -E checking for ANSI C header files... (cached) yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking for inline... inline checking for log in -lm... yes checking for gzread in -lz... yes checking whether /sw/bin/python2.7 version >= 2.6... yes checking for /sw/bin/python2.7 version... 2.7 checking for /sw/bin/python2.7 platform... darwin checking for /sw/bin/python2.7 script directory... ${prefix}/lib/python2.7/site-packages checking for /sw/bin/python2.7 extension module directory... ${exec_prefix}/lib/python2.7/site-packages checking whether to build with debug information... no configure: creating ./config.status config.status: creating Makefile config.status: creating src/libbam/Makefile config.status: creating src/cdflib90/Makefile config.status: creating src/helper_scripts/Makefile config.status: creating src/lofreq_core/Makefile config.status: creating src/lofreq_samtools/Makefile config.status: creating src/lofreq_python/setup_conf.py config.status: creating src/lofreq_python/Makefile config.status: executing depfiles commands config.status: executing libtool commands make Making all in src/cdflib90 gcc -DPACKAGE_NAME=\"Lofreq\" -DPACKAGE_TARNAME=\"lofreq\" -DPACKAGE_VERSION=\"0.6.1\" -DPACKAGE_STRING=\"Lofreq\ 0.6.1\" -DPACKAGE_BUGREPORT=\"wilma@gis.a-star.edu.sg\" -DPACKAGE=\"lofreq\" -DVERSION=\"0.6.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__EXTENSIONS__=1 -D_ALL_SOURCE=1 -D_GNU_SOURCE=1 -D_POSIX_PTHREAD_SEMANTICS=1 -D_TANDEM_SOURCE=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE_LIBM=1 -DHAVE_LIBZ=1 -DNDEBUG=/\*\*/ -D_USE_KNETFILE=/\*\*/ -I. -I/sw/include -Wall -fPIC -g -O2 -MT dcdflib.o -MD -MP -MF .deps/dcdflib.Tpo -c -o dcdflib.o dcdflib.c gcc -DPACKAGE_NAME=\"Lofreq\" -DPACKAGE_TARNAME=\"lofreq\" -DPACKAGE_VERSION=\"0.6.1\" -DPACKAGE_STRING=\"Lofreq\ 0.6.1\" -DPACKAGE_BUGREPORT=\"wilma@gis.a-star.edu.sg\" -DPACKAGE=\"lofreq\" -DVERSION=\"0.6.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__EXTENSIONS__=1 -D_ALL_SOURCE=1 -D_GNU_SOURCE=1 -D_POSIX_PTHREAD_SEMANTICS=1 -D_TANDEM_SOURCE=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE_LIBM=1 -DHAVE_LIBZ=1 -DNDEBUG=/\*\*/ -D_USE_KNETFILE=/\*\*/ -I. -I/sw/include -Wall -fPIC -g -O2 -MT ipmpar.o -MD -MP -MF .deps/ipmpar.Tpo -c -o ipmpar.o ipmpar.c mv -f .deps/ipmpar.Tpo .deps/ipmpar.Po dcdflib.c:1889:36: warning: '&&' within '||' [-Wlogical-op-parentheses] if(!(*s < 0.0e0 || *which != 3 && *s > *xn)) goto S160; ~~ ~~~~~~~~~~~~^~~~~~~~~~~ dcdflib.c:1889:36: note: place parentheses around the '&&' expression to silence this warning if(!(*s < 0.0e0 || *which != 3 && *s > *xn)) goto S160; ^ ( ) dcdflib.c:3551:20: warning: '&&' within '||' [-Wlogical-op-parentheses] if(!(qporq && cum > 1.5e0 || !qporq && ccum > 1.5e0)) goto S280; ~~~~~~^~~~~~~~~~~~~~ ~~ dcdflib.c:3551:20: note: place parentheses around the '&&' expression to silence this warning if(!(qporq && cum > 1.5e0 || !qporq && ccum > 1.5e0)) goto S280; ^ ( ) dcdflib.c:3551:45: warning: '&&' within '||' [-Wlogical-op-parentheses] if(!(qporq && cum > 1.5e0 || !qporq && ccum > 1.5e0)) goto S280; ~~ ~~~~~~~^~~~~~~~~~~~~~~ dcdflib.c:3551:45: note: place parentheses around the '&&' expression to silence this warning if(!(qporq && cum > 1.5e0 || !qporq && ccum > 1.5e0)) goto S280; ^ ( ) dcdflib.c:6410:17: warning: '&&' within '||' [-Wlogical-op-parentheses] qup = qincr && yy < 0.0e0 || !qincr && yy > 0.0e0; ~~~~~~^~~~~~~~~~~~~ ~~ dcdflib.c:6410:17: note: place parentheses around the '&&' expression to silence this warning qup = qincr && yy < 0.0e0 || !qincr && yy > 0.0e0; ^ ( ) dcdflib.c:6410:41: warning: '&&' within '||' [-Wlogical-op-parentheses] qup = qincr && yy < 0.0e0 || !qincr && yy > 0.0e0; ~~ ~~~~~~~^~~~~~~~~~~~~ dcdflib.c:6410:41: note: place parentheses around the '&&' expression to silence this warning qup = qincr && yy < 0.0e0 || !qincr && yy > 0.0e0; ^ ( ) dcdflib.c:6434:18: warning: '&&' within '||' [-Wlogical-op-parentheses] qbdd = qincr && yy >= 0.0e0 || !qincr && yy <= 0.0e0; ~~~~~~^~~~~~~~~~~~~~ ~~ dcdflib.c:6434:18: note: place parentheses around the '&&' expression to silence this warning qbdd = qincr && yy >= 0.0e0 || !qincr && yy <= 0.0e0; ^ ( ) dcdflib.c:6434:43: warning: '&&' within '||' [-Wlogical-op-parentheses] qbdd = qincr && yy >= 0.0e0 || !qincr && yy <= 0.0e0; ~~ ~~~~~~~^~~~~~~~~~~~~~ dcdflib.c:6434:43: note: place parentheses around the '&&' expression to silence this warning qbdd = qincr && yy >= 0.0e0 || !qincr && yy <= 0.0e0; ^ ( ) dcdflib.c:6475:18: warning: '&&' within '||' [-Wlogical-op-parentheses] qbdd = qincr && yy <= 0.0e0 || !qincr && yy >= 0.0e0; ~~~~~~^~~~~~~~~~~~~~ ~~ dcdflib.c:6475:18: note: place parentheses around the '&&' expression to silence this warning qbdd = qincr && yy <= 0.0e0 || !qincr && yy >= 0.0e0; ^ ( ) dcdflib.c:6475:43: warning: '&&' within '||' [-Wlogical-op-parentheses] qbdd = qincr && yy <= 0.0e0 || !qincr && yy >= 0.0e0; ~~ ~~~~~~~^~~~~~~~~~~~~~ dcdflib.c:6475:43: note: place parentheses around the '&&' expression to silence this warning qbdd = qincr && yy <= 0.0e0 || !qincr && yy >= 0.0e0; ^ ( ) dcdflib.c:6877:26: warning: '&&' within '||' [-Wlogical-op-parentheses] qrzero = fc >= 0.0e0 && fb <= 0.0e0 || fc < 0.0e0 && fb >= 0.0e0; ~~~~~~~~~~~~^~~~~~~~~~~~~~ ~~ dcdflib.c:6877:26: note: place parentheses around the '&&' expression to silence this warning qrzero = fc >= 0.0e0 && fb <= 0.0e0 || fc < 0.0e0 && fb >= 0.0e0; ^ ( ) dcdflib.c:6877:55: warning: '&&' within '||' [-Wlogical-op-parentheses] qrzero = fc >= 0.0e0 && fb <= 0.0e0 || fc < 0.0e0 && fb >= 0.0e0; ~~ ~~~~~~~~~~~^~~~~~~~~~~~~~ dcdflib.c:6877:55: note: place parentheses around the '&&' expression to silence this warning qrzero = fc >= 0.0e0 && fb <= 0.0e0 || fc < 0.0e0 && fb >= 0.0e0; ^ ( ) 11 warnings generated. mv -f .deps/dcdflib.Tpo .deps/dcdflib.Po rm -f libcdf.a ar cru libcdf.a dcdflib.o ipmpar.o ranlib libcdf.a Making all in src/libbam gcc -DPACKAGE_NAME=\"Lofreq\" -DPACKAGE_TARNAME=\"lofreq\" -DPACKAGE_VERSION=\"0.6.1\" -DPACKAGE_STRING=\"Lofreq\ 0.6.1\" -DPACKAGE_BUGREPORT=\"wilma@gis.a-star.edu.sg\" -DPACKAGE=\"lofreq\" -DVERSION=\"0.6.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__EXTENSIONS__=1 -D_ALL_SOURCE=1 -D_GNU_SOURCE=1 -D_POSIX_PTHREAD_SEMANTICS=1 -D_TANDEM_SOURCE=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE_LIBM=1 -DHAVE_LIBZ=1 -DNDEBUG=/\*\*/ -D_USE_KNETFILE=/\*\*/ -I. -I/sw/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wall -fPIC -g -O2 -MT bgzf.o -MD -MP -MF .deps/bgzf.Tpo -c -o bgzf.o bgzf.c gcc -DPACKAGE_NAME=\"Lofreq\" -DPACKAGE_TARNAME=\"lofreq\" -DPACKAGE_VERSION=\"0.6.1\" -DPACKAGE_STRING=\"Lofreq\ 0.6.1\" -DPACKAGE_BUGREPORT=\"wilma@gis.a-star.edu.sg\" -DPACKAGE=\"lofreq\" -DVERSION=\"0.6.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__EXTENSIONS__=1 -D_ALL_SOURCE=1 -D_GNU_SOURCE=1 -D_POSIX_PTHREAD_SEMANTICS=1 -D_TANDEM_SOURCE=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE_LIBM=1 -DHAVE_LIBZ=1 -DNDEBUG=/\*\*/ -D_USE_KNETFILE=/\*\*/ -I. -I/sw/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wall -fPIC -g -O2 -MT kstring.o -MD -MP -MF .deps/kstring.Tpo -c -o kstring.o kstring.c gcc -DPACKAGE_NAME=\"Lofreq\" -DPACKAGE_TARNAME=\"lofreq\" -DPACKAGE_VERSION=\"0.6.1\" -DPACKAGE_STRING=\"Lofreq\ 0.6.1\" -DPACKAGE_BUGREPORT=\"wilma@gis.a-star.edu.sg\" -DPACKAGE=\"lofreq\" -DVERSION=\"0.6.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__EXTENSIONS__=1 -D_ALL_SOURCE=1 -D_GNU_SOURCE=1 -D_POSIX_PTHREAD_SEMANTICS=1 -D_TANDEM_SOURCE=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE_LIBM=1 -DHAVE_LIBZ=1 -DNDEBUG=/\*\*/ -D_USE_KNETFILE=/\*\*/ -I. -I/sw/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wall -fPIC -g -O2 -MT bam_aux.o -MD -MP -MF .deps/bam_aux.Tpo -c -o bam_aux.o bam_aux.c gcc -DPACKAGE_NAME=\"Lofreq\" -DPACKAGE_TARNAME=\"lofreq\" -DPACKAGE_VERSION=\"0.6.1\" -DPACKAGE_STRING=\"Lofreq\ 0.6.1\" -DPACKAGE_BUGREPORT=\"wilma@gis.a-star.edu.sg\" -DPACKAGE=\"lofreq\" -DVERSION=\"0.6.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__EXTENSIONS__=1 -D_ALL_SOURCE=1 -D_GNU_SOURCE=1 -D_POSIX_PTHREAD_SEMANTICS=1 -D_TANDEM_SOURCE=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE_LIBM=1 -DHAVE_LIBZ=1 -DNDEBUG=/\*\*/ -D_USE_KNETFILE=/\*\*/ -I. -I/sw/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wall -fPIC -g -O2 -MT bam.o -MD -MP -MF .deps/bam.Tpo -c -o bam.o bam.c gcc -DPACKAGE_NAME=\"Lofreq\" -DPACKAGE_TARNAME=\"lofreq\" -DPACKAGE_VERSION=\"0.6.1\" -DPACKAGE_STRING=\"Lofreq\ 0.6.1\" -DPACKAGE_BUGREPORT=\"wilma@gis.a-star.edu.sg\" -DPACKAGE=\"lofreq\" -DVERSION=\"0.6.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__EXTENSIONS__=1 -D_ALL_SOURCE=1 -D_GNU_SOURCE=1 -D_POSIX_PTHREAD_SEMANTICS=1 -D_TANDEM_SOURCE=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE_LIBM=1 -DHAVE_LIBZ=1 -DNDEBUG=/\*\*/ -D_USE_KNETFILE=/\*\*/ -I. -I/sw/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wall -fPIC -g -O2 -MT bam_import.o -MD -MP -MF .deps/bam_import.Tpo -c -o bam_import.o bam_import.c gcc -DPACKAGE_NAME=\"Lofreq\" -DPACKAGE_TARNAME=\"lofreq\" -DPACKAGE_VERSION=\"0.6.1\" -DPACKAGE_STRING=\"Lofreq\ 0.6.1\" -DPACKAGE_BUGREPORT=\"wilma@gis.a-star.edu.sg\" -DPACKAGE=\"lofreq\" -DVERSION=\"0.6.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__EXTENSIONS__=1 -D_ALL_SOURCE=1 -D_GNU_SOURCE=1 -D_POSIX_PTHREAD_SEMANTICS=1 -D_TANDEM_SOURCE=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE_LIBM=1 -DHAVE_LIBZ=1 -DNDEBUG=/\*\*/ -D_USE_KNETFILE=/\*\*/ -I. -I/sw/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wall -fPIC -g -O2 -MT sam.o -MD -MP -MF .deps/sam.Tpo -c -o sam.o sam.c gcc -DPACKAGE_NAME=\"Lofreq\" -DPACKAGE_TARNAME=\"lofreq\" -DPACKAGE_VERSION=\"0.6.1\" -DPACKAGE_STRING=\"Lofreq\ 0.6.1\" -DPACKAGE_BUGREPORT=\"wilma@gis.a-star.edu.sg\" -DPACKAGE=\"lofreq\" -DVERSION=\"0.6.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__EXTENSIONS__=1 -D_ALL_SOURCE=1 -D_GNU_SOURCE=1 -D_POSIX_PTHREAD_SEMANTICS=1 -D_TANDEM_SOURCE=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE_LIBM=1 -DHAVE_LIBZ=1 -DNDEBUG=/\*\*/ -D_USE_KNETFILE=/\*\*/ -I. -I/sw/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wall -fPIC -g -O2 -MT bam_index.o -MD -MP -MF .deps/bam_index.Tpo -c -o bam_index.o bam_index.c gcc -DPACKAGE_NAME=\"Lofreq\" -DPACKAGE_TARNAME=\"lofreq\" -DPACKAGE_VERSION=\"0.6.1\" -DPACKAGE_STRING=\"Lofreq\ 0.6.1\" -DPACKAGE_BUGREPORT=\"wilma@gis.a-star.edu.sg\" -DPACKAGE=\"lofreq\" -DVERSION=\"0.6.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__EXTENSIONS__=1 -D_ALL_SOURCE=1 -D_GNU_SOURCE=1 -D_POSIX_PTHREAD_SEMANTICS=1 -D_TANDEM_SOURCE=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE_LIBM=1 -DHAVE_LIBZ=1 -DNDEBUG=/\*\*/ -D_USE_KNETFILE=/\*\*/ -I. -I/sw/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wall -fPIC -g -O2 -MT bam_pileup.o -MD -MP -MF .deps/bam_pileup.Tpo -c -o bam_pileup.o bam_pileup.c bam_aux.c:5:1: warning: unused function 'kh_clear_s' [-Wunused-function] KHASH_MAP_INIT_STR(s, int) ^ ./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) ^ ./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) ^ ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :204:1: note: expanded from here kh_clear_s ^ bam_aux.c:5:1: warning: unused function 'kh_del_s' [-Wunused-function] ./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) ^ ./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) ^ ./khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :218:1: note: expanded from here kh_del_s ^ bam_aux.c:6:1: warning: unused function 'kh_init_r2l' [-Wunused-function] KHASH_MAP_INIT_STR(r2l, str_p) ^ ./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) ^ ./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) ^ ./khash.h:168:23: note: expanded from macro 'KHASH_INIT2' SCOPE kh_##name##_t *kh_init_##name() { \ ^ :225:1: note: expanded from here kh_init_r2l ^ bam_aux.c:6:1: warning: unused function 'kh_destroy_r2l' [-Wunused-function] ./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) ^ ./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) ^ ./khash.h:171:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_destroy_##name(kh_##name##_t *h) \ ^ :230:1: note: expanded from here kh_destroy_r2l ^ bam_aux.c:6:1: warning: unused function 'kh_clear_r2l' [-Wunused-function] ./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) ^ ./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) ^ ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :233:1: note: expanded from here kh_clear_r2l ^ bam_aux.c:6:1: warning: unused function 'kh_get_r2l' [-Wunused-function] ./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) ^ ./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) ^ ./khash.h:186:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :236:1: note: expanded from here kh_get_r2l ^ bam_aux.c:6:1: warning: unused function 'kh_put_r2l' [-Wunused-function] ./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) ^ ./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) ^ ./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) \ ^ :242:1: note: expanded from here kh_put_r2l ^ bam_aux.c:6:1: warning: unused function 'kh_del_r2l' [-Wunused-function] ./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) ^ ./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) ^ ./khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :247:1: note: expanded from here kh_del_r2l ^ bam_import.c:18:1: warning: unused function 'kh_clear_ref' [-Wunused-function] KHASH_MAP_INIT_STR(ref, uint64_t) ^ ./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) ^ ./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) ^ ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :204:1: note: expanded from here kh_clear_ref ^ bam_import.c:18:1: warning: unused function 'kh_get_ref' [-Wunused-function] ./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) ^ ./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) ^ ./khash.h:186:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :207:1: note: expanded from here kh_get_ref ^ bam_import.c:18:1: warning: unused function 'kh_del_ref' [-Wunused-function] ./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) ^ ./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) ^ ./khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :218:1: note: expanded from here kh_del_ref ^ bgzf.c:44:1: warning: unused function 'kh_clear_cache' [-Wunused-function] KHASH_MAP_INIT_INT64(cache, cache_t) ^ ./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) ^ ./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) ^ ./khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :11:1: note: expanded from here kh_clear_cache ^ bam_index.c:64:1: warning: unused function 'kh_clear_i' [-Wunused-function] KHASH_MAP_INIT_INT(i, bam_binlist_t) ^ ./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) ^ ./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) ^ ./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 ^ bam_index.c:64:1: warning: unused function 'kh_del_i' [-Wunused-function] ./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) ^ ./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) ^ ./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 ^ mv -f .deps/sam.Tpo .deps/sam.Po mv -f .deps/kstring.Tpo .deps/kstring.Po gcc -DPACKAGE_NAME=\"Lofreq\" -DPACKAGE_TARNAME=\"lofreq\" -DPACKAGE_VERSION=\"0.6.1\" -DPACKAGE_STRING=\"Lofreq\ 0.6.1\" -DPACKAGE_BUGREPORT=\"wilma@gis.a-star.edu.sg\" -DPACKAGE=\"lofreq\" -DVERSION=\"0.6.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__EXTENSIONS__=1 -D_ALL_SOURCE=1 -D_GNU_SOURCE=1 -D_POSIX_PTHREAD_SEMANTICS=1 -D_TANDEM_SOURCE=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE_LIBM=1 -DHAVE_LIBZ=1 -DNDEBUG=/\*\*/ -D_USE_KNETFILE=/\*\*/ -I. -I/sw/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wall -fPIC -g -O2 -MT bam_lpileup.o -MD -MP -MF .deps/bam_lpileup.Tpo -c -o bam_lpileup.o bam_lpileup.c gcc -DPACKAGE_NAME=\"Lofreq\" -DPACKAGE_TARNAME=\"lofreq\" -DPACKAGE_VERSION=\"0.6.1\" -DPACKAGE_STRING=\"Lofreq\ 0.6.1\" -DPACKAGE_BUGREPORT=\"wilma@gis.a-star.edu.sg\" -DPACKAGE=\"lofreq\" -DVERSION=\"0.6.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__EXTENSIONS__=1 -D_ALL_SOURCE=1 -D_GNU_SOURCE=1 -D_POSIX_PTHREAD_SEMANTICS=1 -D_TANDEM_SOURCE=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE_LIBM=1 -DHAVE_LIBZ=1 -DNDEBUG=/\*\*/ -D_USE_KNETFILE=/\*\*/ -I. -I/sw/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wall -fPIC -g -O2 -MT bam_md.o -MD -MP -MF .deps/bam_md.Tpo -c -o bam_md.o bam_md.c mv -f .deps/bam_pileup.Tpo .deps/bam_pileup.Po gcc -DPACKAGE_NAME=\"Lofreq\" -DPACKAGE_TARNAME=\"lofreq\" -DPACKAGE_VERSION=\"0.6.1\" -DPACKAGE_STRING=\"Lofreq\ 0.6.1\" -DPACKAGE_BUGREPORT=\"wilma@gis.a-star.edu.sg\" -DPACKAGE=\"lofreq\" -DVERSION=\"0.6.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__EXTENSIONS__=1 -D_ALL_SOURCE=1 -D_GNU_SOURCE=1 -D_POSIX_PTHREAD_SEMANTICS=1 -D_TANDEM_SOURCE=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE_LIBM=1 -DHAVE_LIBZ=1 -DNDEBUG=/\*\*/ -D_USE_KNETFILE=/\*\*/ -I. -I/sw/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wall -fPIC -g -O2 -MT razf.o -MD -MP -MF .deps/razf.Tpo -c -o razf.o razf.c 8 warnings generated. mv -f .deps/bam_aux.Tpo .deps/bam_aux.Po gcc -DPACKAGE_NAME=\"Lofreq\" -DPACKAGE_TARNAME=\"lofreq\" -DPACKAGE_VERSION=\"0.6.1\" -DPACKAGE_STRING=\"Lofreq\ 0.6.1\" -DPACKAGE_BUGREPORT=\"wilma@gis.a-star.edu.sg\" -DPACKAGE=\"lofreq\" -DVERSION=\"0.6.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__EXTENSIONS__=1 -D_ALL_SOURCE=1 -D_GNU_SOURCE=1 -D_POSIX_PTHREAD_SEMANTICS=1 -D_TANDEM_SOURCE=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE_LIBM=1 -DHAVE_LIBZ=1 -DNDEBUG=/\*\*/ -D_USE_KNETFILE=/\*\*/ -I. -I/sw/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wall -fPIC -g -O2 -MT faidx.o -MD -MP -MF .deps/faidx.Tpo -c -o faidx.o faidx.c 1 warning generated. mv -f .deps/bgzf.Tpo .deps/bgzf.Po gcc -DPACKAGE_NAME=\"Lofreq\" -DPACKAGE_TARNAME=\"lofreq\" -DPACKAGE_VERSION=\"0.6.1\" -DPACKAGE_STRING=\"Lofreq\ 0.6.1\" -DPACKAGE_BUGREPORT=\"wilma@gis.a-star.edu.sg\" -DPACKAGE=\"lofreq\" -DVERSION=\"0.6.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__EXTENSIONS__=1 -D_ALL_SOURCE=1 -D_GNU_SOURCE=1 -D_POSIX_PTHREAD_SEMANTICS=1 -D_TANDEM_SOURCE=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE_LIBM=1 -DHAVE_LIBZ=1 -DNDEBUG=/\*\*/ -D_USE_KNETFILE=/\*\*/ -I. -I/sw/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wall -fPIC -g -O2 -MT bedidx.o -MD -MP -MF .deps/bedidx.Tpo -c -o bedidx.o bedidx.c faidx.c:14:1: warning: unused function 'kh_clear_s' [-Wunused-function] KHASH_MAP_INIT_STR(s, faidx1_t) ^ ./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) ^ ./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) ^ ./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 ^ faidx.c:14:1: warning: unused function 'kh_del_s' [-Wunused-function] ./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) ^ ./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) ^ ./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 ^ bedidx.c:24:1: warning: unused function 'kh_clear_reg' [-Wunused-function] KHASH_MAP_INIT_STR(reg, bed_reglist_t) ^ ./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) ^ ./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) ^ ./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 ^ bedidx.c:24:1: warning: unused function 'kh_del_reg' [-Wunused-function] ./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) ^ ./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) ^ ./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 ^ mv -f .deps/bam_lpileup.Tpo .deps/bam_lpileup.Po gcc -DPACKAGE_NAME=\"Lofreq\" -DPACKAGE_TARNAME=\"lofreq\" -DPACKAGE_VERSION=\"0.6.1\" -DPACKAGE_STRING=\"Lofreq\ 0.6.1\" -DPACKAGE_BUGREPORT=\"wilma@gis.a-star.edu.sg\" -DPACKAGE=\"lofreq\" -DVERSION=\"0.6.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__EXTENSIONS__=1 -D_ALL_SOURCE=1 -D_GNU_SOURCE=1 -D_POSIX_PTHREAD_SEMANTICS=1 -D_TANDEM_SOURCE=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE_LIBM=1 -DHAVE_LIBZ=1 -DNDEBUG=/\*\*/ -D_USE_KNETFILE=/\*\*/ -I. -I/sw/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wall -fPIC -g -O2 -MT knetfile.o -MD -MP -MF .deps/knetfile.Tpo -c -o knetfile.o knetfile.c 3 warnings generated. mv -f .deps/bam_import.Tpo .deps/bam_import.Po gcc -DPACKAGE_NAME=\"Lofreq\" -DPACKAGE_TARNAME=\"lofreq\" -DPACKAGE_VERSION=\"0.6.1\" -DPACKAGE_STRING=\"Lofreq\ 0.6.1\" -DPACKAGE_BUGREPORT=\"wilma@gis.a-star.edu.sg\" -DPACKAGE=\"lofreq\" -DVERSION=\"0.6.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__EXTENSIONS__=1 -D_ALL_SOURCE=1 -D_GNU_SOURCE=1 -D_POSIX_PTHREAD_SEMANTICS=1 -D_TANDEM_SOURCE=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE_LIBM=1 -DHAVE_LIBZ=1 -DNDEBUG=/\*\*/ -D_USE_KNETFILE=/\*\*/ -I. -I/sw/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wall -fPIC -g -O2 -MT sam_header.o -MD -MP -MF .deps/sam_header.Tpo -c -o sam_header.o sam_header.c mv -f .deps/bam.Tpo .deps/bam.Po gcc -DPACKAGE_NAME=\"Lofreq\" -DPACKAGE_TARNAME=\"lofreq\" -DPACKAGE_VERSION=\"0.6.1\" -DPACKAGE_STRING=\"Lofreq\ 0.6.1\" -DPACKAGE_BUGREPORT=\"wilma@gis.a-star.edu.sg\" -DPACKAGE=\"lofreq\" -DVERSION=\"0.6.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__EXTENSIONS__=1 -D_ALL_SOURCE=1 -D_GNU_SOURCE=1 -D_POSIX_PTHREAD_SEMANTICS=1 -D_TANDEM_SOURCE=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE_LIBM=1 -DHAVE_LIBZ=1 -DNDEBUG=/\*\*/ -D_USE_KNETFILE=/\*\*/ -I. -I/sw/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wall -fPIC -g -O2 -MT kprobaln.o -MD -MP -MF .deps/kprobaln.Tpo -c -o kprobaln.o kprobaln.c mv -f .deps/bam_md.Tpo .deps/bam_md.Po mv -f .deps/razf.Tpo .deps/razf.Po sam_header.c:9:1: warning: unused function 'kh_clear_str' [-Wunused-function] KHASH_MAP_INIT_STR(str, const char *) ^ ./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) ^ ./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) ^ ./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 ^ sam_header.c:9:1: warning: unused function 'kh_del_str' [-Wunused-function] ./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) ^ ./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) ^ ./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. mv -f .deps/faidx.Tpo .deps/faidx.Po 2 warnings generated. 2 warnings generated. mv -f .deps/bam_index.Tpo .deps/bam_index.Po mv -f .deps/bedidx.Tpo .deps/bedidx.Po mv -f .deps/kprobaln.Tpo .deps/kprobaln.Po mv -f .deps/knetfile.Tpo .deps/knetfile.Po 2 warnings generated. mv -f .deps/sam_header.Tpo .deps/sam_header.Po rm -f libbam.a ar cru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o sam_header.o kprobaln.o ranlib libbam.a Making all in src/helper_scripts make[1]: Nothing to be done for `all'. Making all in src/lofreq_core gcc -DPACKAGE_NAME=\"Lofreq\" -DPACKAGE_TARNAME=\"lofreq\" -DPACKAGE_VERSION=\"0.6.1\" -DPACKAGE_STRING=\"Lofreq\ 0.6.1\" -DPACKAGE_BUGREPORT=\"wilma@gis.a-star.edu.sg\" -DPACKAGE=\"lofreq\" -DVERSION=\"0.6.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__EXTENSIONS__=1 -D_ALL_SOURCE=1 -D_GNU_SOURCE=1 -D_POSIX_PTHREAD_SEMANTICS=1 -D_TANDEM_SOURCE=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE_LIBM=1 -DHAVE_LIBZ=1 -DNDEBUG=/\*\*/ -D_USE_KNETFILE=/\*\*/ -I. -I/sw/include -Wall -I../cdflib90/ -I../libbam/ -fPIC -g -O2 -MT bam2depth.o -MD -MP -MF .deps/bam2depth.Tpo -c -o bam2depth.o bam2depth.c gcc -DPACKAGE_NAME=\"Lofreq\" -DPACKAGE_TARNAME=\"lofreq\" -DPACKAGE_VERSION=\"0.6.1\" -DPACKAGE_STRING=\"Lofreq\ 0.6.1\" -DPACKAGE_BUGREPORT=\"wilma@gis.a-star.edu.sg\" -DPACKAGE=\"lofreq\" -DVERSION=\"0.6.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__EXTENSIONS__=1 -D_ALL_SOURCE=1 -D_GNU_SOURCE=1 -D_POSIX_PTHREAD_SEMANTICS=1 -D_TANDEM_SOURCE=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE_LIBM=1 -DHAVE_LIBZ=1 -DNDEBUG=/\*\*/ -D_USE_KNETFILE=/\*\*/ -I. -I/sw/include -Wall -I../cdflib90/ -I../libbam/ -fPIC -g -O2 -MT binom.o -MD -MP -MF .deps/binom.Tpo -c -o binom.o binom.c gcc -DPACKAGE_NAME=\"Lofreq\" -DPACKAGE_TARNAME=\"lofreq\" -DPACKAGE_VERSION=\"0.6.1\" -DPACKAGE_STRING=\"Lofreq\ 0.6.1\" -DPACKAGE_BUGREPORT=\"wilma@gis.a-star.edu.sg\" -DPACKAGE=\"lofreq\" -DVERSION=\"0.6.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__EXTENSIONS__=1 -D_ALL_SOURCE=1 -D_GNU_SOURCE=1 -D_POSIX_PTHREAD_SEMANTICS=1 -D_TANDEM_SOURCE=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE_LIBM=1 -DHAVE_LIBZ=1 -DNDEBUG=/\*\*/ -D_USE_KNETFILE=/\*\*/ -I. -I/sw/include -Wall -I../cdflib90/ -I../libbam/ -fPIC -g -O2 -MT fet.o -MD -MP -MF .deps/fet.Tpo -c -o fet.o fet.c gcc -DPACKAGE_NAME=\"Lofreq\" -DPACKAGE_TARNAME=\"lofreq\" -DPACKAGE_VERSION=\"0.6.1\" -DPACKAGE_STRING=\"Lofreq\ 0.6.1\" -DPACKAGE_BUGREPORT=\"wilma@gis.a-star.edu.sg\" -DPACKAGE=\"lofreq\" -DVERSION=\"0.6.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__EXTENSIONS__=1 -D_ALL_SOURCE=1 -D_GNU_SOURCE=1 -D_POSIX_PTHREAD_SEMANTICS=1 -D_TANDEM_SOURCE=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE_LIBM=1 -DHAVE_LIBZ=1 -DNDEBUG=/\*\*/ -D_USE_KNETFILE=/\*\*/ -I. -I/sw/include -Wall -I../cdflib90/ -I../libbam/ -fPIC -g -O2 -MT sam_view.o -MD -MP -MF .deps/sam_view.Tpo -c -o sam_view.o sam_view.c gcc -DPACKAGE_NAME=\"Lofreq\" -DPACKAGE_TARNAME=\"lofreq\" -DPACKAGE_VERSION=\"0.6.1\" -DPACKAGE_STRING=\"Lofreq\ 0.6.1\" -DPACKAGE_BUGREPORT=\"wilma@gis.a-star.edu.sg\" -DPACKAGE=\"lofreq\" -DVERSION=\"0.6.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__EXTENSIONS__=1 -D_ALL_SOURCE=1 -D_GNU_SOURCE=1 -D_POSIX_PTHREAD_SEMANTICS=1 -D_TANDEM_SOURCE=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE_LIBM=1 -DHAVE_LIBZ=1 -DNDEBUG=/\*\*/ -D_USE_KNETFILE=/\*\*/ -I. -I/sw/include -Wall -I../cdflib90/ -I../libbam/ -fPIC -g -O2 -MT snpcaller.o -MD -MP -MF .deps/snpcaller.Tpo -c -o snpcaller.o snpcaller.c gcc -DPACKAGE_NAME=\"Lofreq\" -DPACKAGE_TARNAME=\"lofreq\" -DPACKAGE_VERSION=\"0.6.1\" -DPACKAGE_STRING=\"Lofreq\ 0.6.1\" -DPACKAGE_BUGREPORT=\"wilma@gis.a-star.edu.sg\" -DPACKAGE=\"lofreq\" -DVERSION=\"0.6.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__EXTENSIONS__=1 -D_ALL_SOURCE=1 -D_GNU_SOURCE=1 -D_POSIX_PTHREAD_SEMANTICS=1 -D_TANDEM_SOURCE=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE_LIBM=1 -DHAVE_LIBZ=1 -DNDEBUG=/\*\*/ -D_USE_KNETFILE=/\*\*/ -I. -I/sw/include -Wall -I../cdflib90/ -I../libbam/ -fPIC -g -O2 -MT utils.o -MD -MP -MF .deps/utils.Tpo -c -o utils.o utils.c mv -f .deps/binom.Tpo .deps/binom.Po sam_view.c:164:6: warning: unused variable 'c' [-Wunused-variable] int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, compress_level = -1, is_bamout = 0, is_count = 0; ^ sam_view.c:173:5: warning: array index 1 is past the end of the array (which contains 1 element) [-Warray-bounds] argv[1] = bam_file; ^ ~ sam_view.c:171:5: note: array 'argv' declared here char *argv[1]; ^ mv -f .deps/utils.Tpo .deps/utils.Po sam_view.c:24:1: warning: unused function 'kh_clear_rg' [-Wunused-function] KHASH_SET_INIT_STR(rg) ^ ../libbam/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) ^ ../libbam/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) ^ ../libbam/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :39:1: note: expanded from here kh_clear_rg ^ sam_view.c:24:1: warning: unused function 'kh_del_rg' [-Wunused-function] ../libbam/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) ^ ../libbam/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) ^ ../libbam/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :53:1: note: expanded from here kh_del_rg ^ sam_view.c:362:12: warning: unused function 'usage' [-Wunused-function] static int usage(int is_long_help) ^ mv -f .deps/fet.Tpo .deps/fet.Po mv -f .deps/bam2depth.Tpo .deps/bam2depth.Po mv -f .deps/snpcaller.Tpo .deps/snpcaller.Po 5 warnings generated. mv -f .deps/sam_view.Tpo .deps/sam_view.Po rm -f liblofreq_core.a ar cru liblofreq_core.a bam2depth.o binom.o fet.o sam_view.o snpcaller.o utils.o ../cdflib90/libcdf.a ../libbam/libbam.a ranlib liblofreq_core.a Making all in src/lofreq_samtools gcc -DPACKAGE_NAME=\"Lofreq\" -DPACKAGE_TARNAME=\"lofreq\" -DPACKAGE_VERSION=\"0.6.1\" -DPACKAGE_STRING=\"Lofreq\ 0.6.1\" -DPACKAGE_BUGREPORT=\"wilma@gis.a-star.edu.sg\" -DPACKAGE=\"lofreq\" -DVERSION=\"0.6.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__EXTENSIONS__=1 -D_ALL_SOURCE=1 -D_GNU_SOURCE=1 -D_POSIX_PTHREAD_SEMANTICS=1 -D_TANDEM_SOURCE=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DSTDC_HEADERS=1 -DHAVE_LIBM=1 -DHAVE_LIBZ=1 -DNDEBUG=/\*\*/ -D_USE_KNETFILE=/\*\*/ -I. -I/sw/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wall -I../libbam/ -L../libbam/ -g -O2 -MT bam_plcmd.o -MD -MP -MF .deps/bam_plcmd.Tpo -c -o bam_plcmd.o bam_plcmd.c clang: warning: argument unused during compilation: '-L../libbam/' bam_plcmd.c:308:19: warning: unused function 'printw' [-Wunused-function] static inline int printw(int c, FILE *fp) ^ 1 warning generated. mv -f .deps/bam_plcmd.Tpo .deps/bam_plcmd.Po /bin/sh ../../libtool --tag=CC --mode=link gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wall -I../libbam/ -L../libbam/ -g -O2 -L/sw/lib -o lofreq_samtools bam_plcmd.o ../libbam/libbam.a -lz -lm libtool: link: gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wall -I../libbam/ -g -O2 -o lofreq_samtools bam_plcmd.o -L/sw/build.build/lofreq-0.6.1-1/lofreq-0.6.1/src/libbam -L/sw/lib ../libbam/libbam.a -lz -lm Making all in src/lofreq_python env CFLAGS='-g -O2' LDFLAGS='-L/sw/lib' /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/lofreq copying lofreq/__init__.py -> build/lib.macosx-10.9-x86_64-2.7/lofreq copying lofreq/conf.py -> build/lib.macosx-10.9-x86_64-2.7/lofreq copying lofreq/em.py -> build/lib.macosx-10.9-x86_64-2.7/lofreq copying lofreq/fasta_parser.py -> build/lib.macosx-10.9-x86_64-2.7/lofreq copying lofreq/multiple_testing.py -> build/lib.macosx-10.9-x86_64-2.7/lofreq copying lofreq/posmap.py -> build/lib.macosx-10.9-x86_64-2.7/lofreq copying lofreq/qual.py -> build/lib.macosx-10.9-x86_64-2.7/lofreq copying lofreq/sam.py -> build/lib.macosx-10.9-x86_64-2.7/lofreq copying lofreq/simple_vcf.py -> build/lib.macosx-10.9-x86_64-2.7/lofreq copying lofreq/snp.py -> build/lib.macosx-10.9-x86_64-2.7/lofreq copying lofreq/utils.py -> build/lib.macosx-10.9-x86_64-2.7/lofreq running build_ext building 'lofreq_ext' extension creating build/temp.macosx-10.9-x86_64-2.7 creating build/temp.macosx-10.9-x86_64-2.7/lofreq_ext gcc -DNDEBUG -g -fwrapv -fwrapv -O3 -Wall -Wstrict-prototypes -g -O2 -I/sw/include -DNDEBUG=1 -I../cdflib90 -I../lofreq_core -I/sw/include/python2.7 -c lofreq_ext/lofreq_ext.c -o build/temp.macosx-10.9-x86_64-2.7/lofreq_ext/lofreq_ext.o -O3 -funroll-loops lofreq_ext/lofreq_ext.c:264:26: warning: 'tmpnam' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of tmpnam(3), it is highly recommended that you use mkstemp(3) instead. [-Wdeprecated-declarations] svo->fn_out = strdup(tmpnam(NULL)); ^ /usr/include/stdio.h:274:7: note: 'tmpnam' declared here char *tmpnam(char *); ^ 1 warning generated. gcc -L/sw/lib -bundle -L/sw/lib/python2.7/config -lpython2.7 -L/sw/lib -L/sw/lib -g -O2 -I/sw/include build/temp.macosx-10.9-x86_64-2.7/lofreq_ext/lofreq_ext.o ../lofreq_core/liblofreq_core.a ../cdflib90/libcdf.a ../libbam/libbam.a -L/sw/lib -lz -o build/lib.macosx-10.9-x86_64-2.7/lofreq_ext.so running build_scripts creating build/scripts-2.7 copying and adjusting scripts/lofreq_alnoffset.py -> build/scripts-2.7 copying and adjusting scripts/lofreq_bonf.py -> build/scripts-2.7 copying and adjusting scripts/lofreq_diff.py -> build/scripts-2.7 copying and adjusting scripts/lofreq_filter.py -> build/scripts-2.7 copying and adjusting scripts/lofreq_pileup_summary.py -> build/scripts-2.7 copying and adjusting scripts/lofreq_regionbed.py -> build/scripts-2.7 copying and adjusting scripts/lofreq_snpcaller.py -> build/scripts-2.7 copying and adjusting scripts/lofreq_uniq.py -> build/scripts-2.7 copying and adjusting scripts/lofreq_uniq_pipeline.py -> build/scripts-2.7 copying and adjusting scripts/lofreq_varpos_to_vcf.py -> build/scripts-2.7 copying and adjusting scripts/lofreq_version.py -> build/scripts-2.7 changing mode of build/scripts-2.7/lofreq_alnoffset.py from 644 to 755 changing mode of build/scripts-2.7/lofreq_bonf.py from 644 to 755 changing mode of build/scripts-2.7/lofreq_diff.py from 644 to 755 changing mode of build/scripts-2.7/lofreq_filter.py from 644 to 755 changing mode of build/scripts-2.7/lofreq_pileup_summary.py from 644 to 755 changing mode of build/scripts-2.7/lofreq_regionbed.py from 644 to 755 changing mode of build/scripts-2.7/lofreq_snpcaller.py from 644 to 755 changing mode of build/scripts-2.7/lofreq_uniq.py from 644 to 755 changing mode of build/scripts-2.7/lofreq_uniq_pipeline.py from 644 to 755 changing mode of build/scripts-2.7/lofreq_varpos_to_vcf.py from 644 to 755 changing mode of build/scripts-2.7/lofreq_version.py from 644 to 755 make[1]: Nothing to be done for `all-am'. /bin/rm -rf /sw/build.build/root-lofreq-0.6.1-1 /bin/mkdir -p /sw/build.build/root-lofreq-0.6.1-1/sw /bin/mkdir -p /sw/build.build/root-lofreq-0.6.1-1/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-lofreq-0.6.1-1 sudo -u fink-bld [ENV] sh -c /tmp/fink.YWkUE /tmp/fink.NyU2C #!/bin/sh -ev make -w install DESTDIR=/sw/build.build/root-lofreq-0.6.1-1 make: Entering directory `/sw/build.build/lofreq-0.6.1-1/lofreq-0.6.1' Making install in src/cdflib90 make[1]: Entering directory `/sw/build.build/lofreq-0.6.1-1/lofreq-0.6.1/src/cdflib90' make[2]: Entering directory `/sw/build.build/lofreq-0.6.1-1/lofreq-0.6.1/src/cdflib90' make[2]: Nothing to be done for `install-exec-am'. make[2]: Nothing to be done for `install-data-am'. make[2]: Leaving directory `/sw/build.build/lofreq-0.6.1-1/lofreq-0.6.1/src/cdflib90' make[1]: Leaving directory `/sw/build.build/lofreq-0.6.1-1/lofreq-0.6.1/src/cdflib90' Making install in src/libbam make[1]: Entering directory `/sw/build.build/lofreq-0.6.1-1/lofreq-0.6.1/src/libbam' make[2]: Entering directory `/sw/build.build/lofreq-0.6.1-1/lofreq-0.6.1/src/libbam' make[2]: Nothing to be done for `install-exec-am'. make[2]: Nothing to be done for `install-data-am'. make[2]: Leaving directory `/sw/build.build/lofreq-0.6.1-1/lofreq-0.6.1/src/libbam' make[1]: Leaving directory `/sw/build.build/lofreq-0.6.1-1/lofreq-0.6.1/src/libbam' Making install in src/helper_scripts make[1]: Entering directory `/sw/build.build/lofreq-0.6.1-1/lofreq-0.6.1/src/helper_scripts' make[2]: Entering directory `/sw/build.build/lofreq-0.6.1-1/lofreq-0.6.1/src/helper_scripts' test -z "/sw/bin" || ../.././install-sh -c -d "/sw/build.build/root-lofreq-0.6.1-1/sw/bin" /usr/bin/install -c base_qual_calib_wrapper.sh bwa_unique.sh '/sw/build.build/root-lofreq-0.6.1-1/sw/bin' make[2]: Nothing to be done for `install-data-am'. make[2]: Leaving directory `/sw/build.build/lofreq-0.6.1-1/lofreq-0.6.1/src/helper_scripts' make[1]: Leaving directory `/sw/build.build/lofreq-0.6.1-1/lofreq-0.6.1/src/helper_scripts' Making install in src/lofreq_core make[1]: Entering directory `/sw/build.build/lofreq-0.6.1-1/lofreq-0.6.1/src/lofreq_core' make[2]: Entering directory `/sw/build.build/lofreq-0.6.1-1/lofreq-0.6.1/src/lofreq_core' make[2]: Nothing to be done for `install-exec-am'. make[2]: Nothing to be done for `install-data-am'. make[2]: Leaving directory `/sw/build.build/lofreq-0.6.1-1/lofreq-0.6.1/src/lofreq_core' make[1]: Leaving directory `/sw/build.build/lofreq-0.6.1-1/lofreq-0.6.1/src/lofreq_core' Making install in src/lofreq_samtools make[1]: Entering directory `/sw/build.build/lofreq-0.6.1-1/lofreq-0.6.1/src/lofreq_samtools' make[2]: Entering directory `/sw/build.build/lofreq-0.6.1-1/lofreq-0.6.1/src/lofreq_samtools' test -z "/sw/bin" || ../.././install-sh -c -d "/sw/build.build/root-lofreq-0.6.1-1/sw/bin" /bin/sh ../../libtool --mode=install /usr/bin/install -c lofreq_samtools '/sw/build.build/root-lofreq-0.6.1-1/sw/bin' libtool: install: /usr/bin/install -c lofreq_samtools /sw/build.build/root-lofreq-0.6.1-1/sw/bin/lofreq_samtools make[2]: Nothing to be done for `install-data-am'. make[2]: Leaving directory `/sw/build.build/lofreq-0.6.1-1/lofreq-0.6.1/src/lofreq_samtools' make[1]: Leaving directory `/sw/build.build/lofreq-0.6.1-1/lofreq-0.6.1/src/lofreq_samtools' Making install in src/lofreq_python make[1]: Entering directory `/sw/build.build/lofreq-0.6.1-1/lofreq-0.6.1/src/lofreq_python' make[2]: Entering directory `/sw/build.build/lofreq-0.6.1-1/lofreq-0.6.1/src/lofreq_python' /Applications/Xcode.app/Contents/Developer/usr/bin/make install-exec-hook make[3]: Entering directory `/sw/build.build/lofreq-0.6.1-1/lofreq-0.6.1/src/lofreq_python' env CFLAGS='-g -O2' LDFLAGS='-L/sw/lib' /sw/bin/python2.7 setup.py install --prefix '/sw' --root /sw/build.build/root-lofreq-0.6.1-1 running install running build running build_py running build_ext running build_scripts running install_lib creating /sw/build.build/root-lofreq-0.6.1-1/sw/lib creating /sw/build.build/root-lofreq-0.6.1-1/sw/lib/python2.7 creating /sw/build.build/root-lofreq-0.6.1-1/sw/lib/python2.7/site-packages creating /sw/build.build/root-lofreq-0.6.1-1/sw/lib/python2.7/site-packages/lofreq copying build/lib.macosx-10.9-x86_64-2.7/lofreq/__init__.py -> /sw/build.build/root-lofreq-0.6.1-1/sw/lib/python2.7/site-packages/lofreq copying build/lib.macosx-10.9-x86_64-2.7/lofreq/conf.py -> /sw/build.build/root-lofreq-0.6.1-1/sw/lib/python2.7/site-packages/lofreq copying build/lib.macosx-10.9-x86_64-2.7/lofreq/em.py -> /sw/build.build/root-lofreq-0.6.1-1/sw/lib/python2.7/site-packages/lofreq copying build/lib.macosx-10.9-x86_64-2.7/lofreq/fasta_parser.py -> /sw/build.build/root-lofreq-0.6.1-1/sw/lib/python2.7/site-packages/lofreq copying build/lib.macosx-10.9-x86_64-2.7/lofreq/multiple_testing.py -> /sw/build.build/root-lofreq-0.6.1-1/sw/lib/python2.7/site-packages/lofreq copying build/lib.macosx-10.9-x86_64-2.7/lofreq/posmap.py -> /sw/build.build/root-lofreq-0.6.1-1/sw/lib/python2.7/site-packages/lofreq copying build/lib.macosx-10.9-x86_64-2.7/lofreq/qual.py -> /sw/build.build/root-lofreq-0.6.1-1/sw/lib/python2.7/site-packages/lofreq copying build/lib.macosx-10.9-x86_64-2.7/lofreq/sam.py -> /sw/build.build/root-lofreq-0.6.1-1/sw/lib/python2.7/site-packages/lofreq copying build/lib.macosx-10.9-x86_64-2.7/lofreq/simple_vcf.py -> /sw/build.build/root-lofreq-0.6.1-1/sw/lib/python2.7/site-packages/lofreq copying build/lib.macosx-10.9-x86_64-2.7/lofreq/snp.py -> /sw/build.build/root-lofreq-0.6.1-1/sw/lib/python2.7/site-packages/lofreq copying build/lib.macosx-10.9-x86_64-2.7/lofreq/utils.py -> /sw/build.build/root-lofreq-0.6.1-1/sw/lib/python2.7/site-packages/lofreq copying build/lib.macosx-10.9-x86_64-2.7/lofreq_ext.so -> /sw/build.build/root-lofreq-0.6.1-1/sw/lib/python2.7/site-packages byte-compiling /sw/build.build/root-lofreq-0.6.1-1/sw/lib/python2.7/site-packages/lofreq/__init__.py to __init__.pyc byte-compiling /sw/build.build/root-lofreq-0.6.1-1/sw/lib/python2.7/site-packages/lofreq/conf.py to conf.pyc byte-compiling /sw/build.build/root-lofreq-0.6.1-1/sw/lib/python2.7/site-packages/lofreq/em.py to em.pyc byte-compiling /sw/build.build/root-lofreq-0.6.1-1/sw/lib/python2.7/site-packages/lofreq/fasta_parser.py to fasta_parser.pyc byte-compiling /sw/build.build/root-lofreq-0.6.1-1/sw/lib/python2.7/site-packages/lofreq/multiple_testing.py to multiple_testing.pyc byte-compiling /sw/build.build/root-lofreq-0.6.1-1/sw/lib/python2.7/site-packages/lofreq/posmap.py to posmap.pyc byte-compiling /sw/build.build/root-lofreq-0.6.1-1/sw/lib/python2.7/site-packages/lofreq/qual.py to qual.pyc byte-compiling /sw/build.build/root-lofreq-0.6.1-1/sw/lib/python2.7/site-packages/lofreq/sam.py to sam.pyc byte-compiling /sw/build.build/root-lofreq-0.6.1-1/sw/lib/python2.7/site-packages/lofreq/simple_vcf.py to simple_vcf.pyc byte-compiling /sw/build.build/root-lofreq-0.6.1-1/sw/lib/python2.7/site-packages/lofreq/snp.py to snp.pyc byte-compiling /sw/build.build/root-lofreq-0.6.1-1/sw/lib/python2.7/site-packages/lofreq/utils.py to utils.pyc running install_scripts copying build/scripts-2.7/lofreq_alnoffset.py -> /sw/build.build/root-lofreq-0.6.1-1/sw/bin copying build/scripts-2.7/lofreq_bonf.py -> /sw/build.build/root-lofreq-0.6.1-1/sw/bin copying build/scripts-2.7/lofreq_diff.py -> /sw/build.build/root-lofreq-0.6.1-1/sw/bin copying build/scripts-2.7/lofreq_filter.py -> /sw/build.build/root-lofreq-0.6.1-1/sw/bin copying build/scripts-2.7/lofreq_pileup_summary.py -> /sw/build.build/root-lofreq-0.6.1-1/sw/bin copying build/scripts-2.7/lofreq_regionbed.py -> /sw/build.build/root-lofreq-0.6.1-1/sw/bin copying build/scripts-2.7/lofreq_snpcaller.py -> /sw/build.build/root-lofreq-0.6.1-1/sw/bin copying build/scripts-2.7/lofreq_uniq.py -> /sw/build.build/root-lofreq-0.6.1-1/sw/bin copying build/scripts-2.7/lofreq_uniq_pipeline.py -> /sw/build.build/root-lofreq-0.6.1-1/sw/bin copying build/scripts-2.7/lofreq_varpos_to_vcf.py -> /sw/build.build/root-lofreq-0.6.1-1/sw/bin copying build/scripts-2.7/lofreq_version.py -> /sw/build.build/root-lofreq-0.6.1-1/sw/bin changing mode of /sw/build.build/root-lofreq-0.6.1-1/sw/bin/lofreq_alnoffset.py to 755 changing mode of /sw/build.build/root-lofreq-0.6.1-1/sw/bin/lofreq_bonf.py to 755 changing mode of /sw/build.build/root-lofreq-0.6.1-1/sw/bin/lofreq_diff.py to 755 changing mode of /sw/build.build/root-lofreq-0.6.1-1/sw/bin/lofreq_filter.py to 755 changing mode of /sw/build.build/root-lofreq-0.6.1-1/sw/bin/lofreq_pileup_summary.py to 755 changing mode of /sw/build.build/root-lofreq-0.6.1-1/sw/bin/lofreq_regionbed.py to 755 changing mode of /sw/build.build/root-lofreq-0.6.1-1/sw/bin/lofreq_snpcaller.py to 755 changing mode of /sw/build.build/root-lofreq-0.6.1-1/sw/bin/lofreq_uniq.py to 755 changing mode of /sw/build.build/root-lofreq-0.6.1-1/sw/bin/lofreq_uniq_pipeline.py to 755 changing mode of /sw/build.build/root-lofreq-0.6.1-1/sw/bin/lofreq_varpos_to_vcf.py to 755 changing mode of /sw/build.build/root-lofreq-0.6.1-1/sw/bin/lofreq_version.py to 755 running install_egg_info Writing /sw/build.build/root-lofreq-0.6.1-1/sw/lib/python2.7/site-packages/Lofreq-0.6.1-py2.7.egg-info make[3]: Leaving directory `/sw/build.build/lofreq-0.6.1-1/lofreq-0.6.1/src/lofreq_python' make[2]: Nothing to be done for `install-data-am'. make[2]: Leaving directory `/sw/build.build/lofreq-0.6.1-1/lofreq-0.6.1/src/lofreq_python' make[1]: Leaving directory `/sw/build.build/lofreq-0.6.1-1/lofreq-0.6.1/src/lofreq_python' make[1]: Entering directory `/sw/build.build/lofreq-0.6.1-1/lofreq-0.6.1' make[2]: Entering directory `/sw/build.build/lofreq-0.6.1-1/lofreq-0.6.1' make[2]: Nothing to be done for `install-exec-am'. make[2]: Nothing to be done for `install-data-am'. make[2]: Leaving directory `/sw/build.build/lofreq-0.6.1-1/lofreq-0.6.1' make[1]: Leaving directory `/sw/build.build/lofreq-0.6.1-1/lofreq-0.6.1' make: Leaving directory `/sw/build.build/lofreq-0.6.1-1/lofreq-0.6.1' sudo -u fink-bld [ENV] sh -c /tmp/fink.GbTX9 /usr/bin/install -d -m 700 /sw/build.build/root-lofreq-0.6.1-1/sw/share/doc/lofreq /bin/cp -r AUTHORS /sw/build.build/root-lofreq-0.6.1-1/sw/share/doc/lofreq/ /bin/cp -r COPYING /sw/build.build/root-lofreq-0.6.1-1/sw/share/doc/lofreq/ /bin/cp -r ChangeLog /sw/build.build/root-lofreq-0.6.1-1/sw/share/doc/lofreq/ /bin/cp -r NEWS /sw/build.build/root-lofreq-0.6.1-1/sw/share/doc/lofreq/ /bin/cp -r README /sw/build.build/root-lofreq-0.6.1-1/sw/share/doc/lofreq/ /bin/chmod -R go=u-w /sw/build.build/root-lofreq-0.6.1-1/sw/share/doc/lofreq /bin/rm -f /sw/build.build/root-lofreq-0.6.1-1/sw/info/dir /sw/build.build/root-lofreq-0.6.1-1/sw/info/dir.old /sw/build.build/root-lofreq-0.6.1-1/sw/share/info/dir /sw/build.build/root-lofreq-0.6.1-1/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-lofreq-0.6.1-1 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `lofreq' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/lofreq_0.6.1-1_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-lofreq-0.6.1-1 (Reading database ... 12613 files and directories currently installed.) Removing fink-buildlock-lofreq-0.6.1-1 ...