printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild breseq 2>&1 The package 'breseq' will be built without being installed. Reading build dependency for breseq-0.23-1... Reading dependency for breseq-0.23-1... Reading build conflict for breseq-0.23-1... The package 'fink-package-precedence' will be installed. Reading dependency for fink-package-precedence-0.18-1... Reading runtime dependency for fink-package-precedence-0.18-1... The package 'gcc48-compiler' will be installed. Reading dependency for gcc48-compiler-4.8.3-1000... Reading runtime dependency for gcc48-compiler-4.8.3-1000... The package 'libncurses5' will be installed. Reading dependency for libncurses5-5.9-20110507-1... Reading runtime dependency for libncurses5-5.9-20110507-1... The package 'bowtie2' will be installed. Reading dependency for bowtie2-2.2.2-2... Reading runtime dependency for bowtie2-2.2.2-2... The package 'gcc48-shlibs' will be installed. Reading dependency for gcc48-shlibs-4.8.3-1000... Reading runtime dependency for gcc48-shlibs-4.8.3-1000... The package 'r-base' will be installed. Reading dependency for r-base-3.1.1-2... Reading runtime dependency for r-base-3.1.1-2... The package 'gmp5-shlibs' will be installed. Reading dependency for gmp5-shlibs-6.0.0a-1... Reading runtime dependency for gmp5-shlibs-6.0.0a-1... The package 'libgmpxx5-shlibs' will be installed. Reading dependency for libgmpxx5-shlibs-6.0.0a-1... Reading runtime dependency for libgmpxx5-shlibs-6.0.0a-1... The package 'libmpfr4-shlibs' will be installed. Reading dependency for libmpfr4-shlibs-3.1.2-1... Reading runtime dependency for libmpfr4-shlibs-3.1.2-1... The package 'cloog-org2-shlibs' will be installed. Reading dependency for cloog-org2-shlibs-0.18.2-1... Reading runtime dependency for cloog-org2-shlibs-0.18.2-1... The package 'isl-shlibs' will be installed. Reading dependency for isl-shlibs-0.12.2-2... Reading runtime dependency for isl-shlibs-0.12.2-2... The package 'libmpc3-shlibs' will be installed. Reading dependency for libmpc3-shlibs-1.0.2-1... Reading runtime dependency for libmpc3-shlibs-1.0.2-1... The package 'r-base31' will be installed. Reading dependency for r-base31-3.1.1-2... Reading runtime dependency for r-base31-3.1.1-2... The package 'r-base31-shlibs' will be installed. Reading dependency for r-base31-shlibs-3.1.1-2... Reading runtime dependency for r-base31-shlibs-3.1.1-2... The package 'flag-sort' will be installed. Reading dependency for flag-sort-0.5-1... Reading runtime dependency for flag-sort-0.5-1... The package 'cairo-shlibs' will be installed. Reading dependency for cairo-shlibs-1.12.14-1... Reading runtime dependency for cairo-shlibs-1.12.14-1... The package 'gcc49-shlibs' will be installed. Reading dependency for gcc49-shlibs-4.9.1-1000... Reading runtime dependency for gcc49-shlibs-4.9.1-1000... The package 'glib2-shlibs' will be installed. Reading dependency for glib2-shlibs-2.22.4-8... Reading runtime dependency for glib2-shlibs-2.22.4-8... The package 'libicu48-shlibs' will be installed. Reading dependency for libicu48-shlibs-4.8.1.1-2... Reading runtime dependency for libicu48-shlibs-4.8.1.1-2... The package 'libjpeg9-shlibs' will be installed. Reading dependency for libjpeg9-shlibs-9a-1... Reading runtime dependency for libjpeg9-shlibs-9a-1... The package 'liblzma5-shlibs' will be installed. Reading dependency for liblzma5-shlibs-5.0.5-2... Reading runtime dependency for liblzma5-shlibs-5.0.5-2... The package 'libpng16-shlibs' will be installed. Reading dependency for libpng16-shlibs-1.6.12-1... Reading runtime dependency for libpng16-shlibs-1.6.12-1... The package 'libtiff5-shlibs' will be installed. Reading dependency for libtiff5-shlibs-4.0.3-5... Reading runtime dependency for libtiff5-shlibs-4.0.3-5... The package 'pango1-xft2-ft219-shlibs' will be installed. Reading dependency for pango1-xft2-ft219-shlibs-1.24.5-9... Reading runtime dependency for pango1-xft2-ft219-shlibs-1.24.5-9... The package 'libpcre1-shlibs' will be installed. Reading dependency for libpcre1-shlibs-8.35-1... Reading runtime dependency for libpcre1-shlibs-8.35-1... 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 'tcltk' will be installed. Reading dependency for tcltk-8.6.1-104... Reading runtime dependency for tcltk-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 'pixman-shlibs' will be installed. Reading dependency for pixman-shlibs-0.32.4-1... Reading runtime dependency for pixman-shlibs-0.32.4-1... The package 'xdg-base' will be installed. Reading dependency for xdg-base-0.8-2... Reading runtime dependency for xdg-base-0.8-2... The package 'libjbig-shlibs' will be installed. Reading dependency for libjbig-shlibs-2.0-1... Reading runtime dependency for libjbig-shlibs-2.0-1... The package 'libthai-shlibs' will be installed. Reading dependency for libthai-shlibs-0.1.20-1... Reading runtime dependency for libthai-shlibs-0.1.20-1... 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 '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 '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 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 'libdatrie1-shlibs' will be installed. Reading dependency for libdatrie1-shlibs-0.2.8-2... Reading runtime dependency for libdatrie1-shlibs-0.2.8-2... The package 'libthai' will be installed. Reading dependency for libthai-0.1.20-1... Reading runtime dependency for libthai-0.1.20-1... The following package will be rebuilt: breseq The following 39 additional packages will be installed: bowtie2 cairo-shlibs cloog-org2-shlibs expat1-shlibs fink-package-precedence flag-sort fontconfig-config fontconfig2-shlibs freetype219-shlibs gcc48-compiler gcc48-shlibs gcc49-shlibs glib2-shlibs gmp5-shlibs isl-shlibs libdatrie1-shlibs libgmpxx5-shlibs libicu48-shlibs libjbig-shlibs libjpeg9-shlibs liblzma5-shlibs libmpc3-shlibs libmpfr4-shlibs libncurses5 libpcre1-shlibs libpng16-shlibs libthai libthai-shlibs libtiff5-shlibs pango1-xft2-ft219-shlibs pixman-shlibs r-base r-base31 r-base31-shlibs readline6-shlibs tcltk tcltk-shlibs xdg-base 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/breseq-0.23.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 0 9497k 0 41747 0 0 101k 0 0:01:33 --:--:-- 0:01:33 101k 9 9497k 9 870k 0 0 643k 0 0:00:14 0:00:01 0:00:13 643k 22 9497k 22 2093k 0 0 896k 0 0:00:10 0:00:02 0:00:08 896k 35 9497k 35 3406k 0 0 903k 0 0:00:10 0:00:03 0:00:07 903k 37 9497k 37 3551k 0 0 818k 0 0:00:11 0:00:04 0:00:07 818k 38 9497k 38 3615k 0 0 673k 0 0:00:14 0:00:05 0:00:09 719k 41 9497k 41 3931k 0 0 569k 0 0:00:16 0:00:06 0:00:10 551k 45 9497k 45 4282k 0 0 532k 0 0:00:17 0:00:08 0:00:09 383k 49 9497k 49 4704k 0 0 564k 0 0:00:16 0:00:08 0:00:08 284k 57 9497k 57 5499k 0 0 588k 0 0:00:16 0:00:09 0:00:07 388k 66 9497k 66 6344k 0 0 612k 0 0:00:15 0:00:10 0:00:05 546k 73 9497k 73 7014k 0 0 595k 0 0:00:15 0:00:11 0:00:04 633k 78 9497k 78 7408k 0 0 600k 0 0:00:15 0:00:12 0:00:03 727k 85 9497k 85 8140k 0 0 610k 0 0:00:15 0:00:13 0:00:02 687k 94 9497k 94 8955k 0 0 623k 0 0:00:15 0:00:14 0:00:01 691k 100 9497k 100 9497k 0 0 633k 0 0:00:14 0:00:14 --:--:-- 681k Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/bowtie2_2.2.2-2_darwin-x86_64.deb Selecting previously deselected package bowtie2. (Reading database ... 4296 files and directories currently installed.) Unpacking bowtie2 (from .../bowtie2_2.2.2-2_darwin-x86_64.deb) ... Setting up bowtie2 (2.2.2-2) ... 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 ... 4358 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/debs/fink-package-precedence_0.18-1_darwin-x86_64.deb Selecting previously deselected package fink-package-precedence. (Reading database ... 4363 files and directories currently installed.) Unpacking fink-package-precedence (from .../fink-package-precedence_0.18-1_darwin-x86_64.deb) ... Setting up fink-package-precedence (0.18-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/flag-sort_0.5-1_darwin-x86_64.deb Selecting previously deselected package flag-sort. (Reading database ... 4364 files and directories currently installed.) Unpacking flag-sort (from .../flag-sort_0.5-1_darwin-x86_64.deb) ... Setting up flag-sort (0.5-1) ... 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 ... 4365 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/languages/gcc49-shlibs_4.9.1-1000_darwin-x86_64.deb Selecting previously deselected package gcc49-shlibs. (Reading database ... 4376 files and directories currently installed.) Unpacking gcc49-shlibs (from .../gcc49-shlibs_4.9.1-1000_darwin-x86_64.deb) ... Setting up gcc49-shlibs (4.9.1-1000) ... 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/libs/libdatrie1-shlibs_0.2.8-2_darwin-x86_64.deb Selecting previously deselected package libdatrie1-shlibs. (Reading database ... 4421 files and directories currently installed.) Unpacking libdatrie1-shlibs (from .../libdatrie1-shlibs_0.2.8-2_darwin-x86_64.deb) ... Setting up libdatrie1-shlibs (0.2.8-2) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/libgmpxx5-shlibs_6.0.0a-1_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/gmp5-shlibs_6.0.0a-1_darwin-x86_64.deb Selecting previously deselected package libgmpxx5-shlibs. (Reading database ... 4428 files and directories currently installed.) Unpacking libgmpxx5-shlibs (from .../libgmpxx5-shlibs_6.0.0a-1_darwin-x86_64.deb) ... Selecting previously deselected package gmp5-shlibs. Unpacking gmp5-shlibs (from .../gmp5-shlibs_6.0.0a-1_darwin-x86_64.deb) ... Setting up gmp5-shlibs (6.0.0a-1) ... Setting up libgmpxx5-shlibs (6.0.0a-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/libicu48-shlibs_4.8.1.1-2_darwin-x86_64.deb Selecting previously deselected package libicu48-shlibs. 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All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/graphics/libpng16-shlibs_1.6.12-1_darwin-x86_64.deb Selecting previously deselected package libpng16-shlibs. (Reading database ... 4567 files and directories currently installed.) Unpacking libpng16-shlibs (from .../libpng16-shlibs_1.6.12-1_darwin-x86_64.deb) ... Setting up libpng16-shlibs (1.6.12-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/libthai-shlibs_0.1.20-1_darwin-x86_64.deb /sw/fink/debs/libthai_0.1.20-1_darwin-x86_64.deb Selecting previously deselected package libthai-shlibs. (Reading database ... 4575 files and directories currently installed.) Unpacking libthai-shlibs (from .../libthai-shlibs_0.1.20-1_darwin-x86_64.deb) ... Selecting previously deselected package libthai. Unpacking libthai (from .../libthai_0.1.20-1_darwin-x86_64.deb) ... Setting up libthai (0.1.20-1) ... Setting up libthai-shlibs (0.1.20-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/libtiff5-shlibs_4.0.3-5_darwin-x86_64.deb Selecting previously deselected package libtiff5-shlibs. (Reading database ... 4590 files and directories currently installed.) Unpacking libtiff5-shlibs (from .../libtiff5-shlibs_4.0.3-5_darwin-x86_64.deb) ... Setting up libtiff5-shlibs (4.0.3-5) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/graphics/pixman-shlibs_0.32.4-1_darwin-x86_64.deb Selecting previously deselected package pixman-shlibs. (Reading database ... 4595 files and directories currently installed.) Unpacking pixman-shlibs (from .../pixman-shlibs_0.32.4-1_darwin-x86_64.deb) ... Setting up pixman-shlibs (0.32.4-1) ... Reading buildlock packages... 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Unpacking gcc48-shlibs (from .../gcc48-shlibs_4.8.3-1000_darwin-x86_64.deb) ... Setting up gcc48-shlibs (4.8.3-1000) ... Clearing dependency_libs of .la files being installed Setting up gcc48-compiler (4.8.3-1000) ... 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/gnome/pango1-xft2-ft219-shlibs_1.24.5-9_darwin-x86_64.deb Selecting previously deselected package pango1-xft2-ft219-shlibs. (Reading database ... 10377 files and directories currently installed.) Unpacking pango1-xft2-ft219-shlibs (from .../pango1-xft2-ft219-shlibs_1.24.5-9_darwin-x86_64.deb) ... Setting up pango1-xft2-ft219-shlibs (1.24.5-9) ... Clearing dependency_libs of .la files being installed 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 ... 10421 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/sci/r-base_3.1.1-2_darwin-x86_64.deb /sw/fink/debs/r-base31_3.1.1-2_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/sci/r-base31-shlibs_3.1.1-2_darwin-x86_64.deb Selecting previously deselected package r-base. (Reading database ... 10897 files and directories currently installed.) Unpacking r-base (from .../r-base_3.1.1-2_darwin-x86_64.deb) ... Selecting previously deselected package r-base31. Unpacking r-base31 (from .../r-base31_3.1.1-2_darwin-x86_64.deb) ... Selecting previously deselected package r-base31-shlibs. Unpacking r-base31-shlibs (from .../r-base31-shlibs_3.1.1-2_darwin-x86_64.deb) ... Setting up r-base31-shlibs (3.1.1-2) ... Setting up r-base31 (3.1.1-2) ... Setting up r-base (3.1.1-2) ... Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-breseq-0.23-1 /sw/build.build dpkg-deb: building package `fink-buildlock-breseq-0.23-1' in `/sw/build.build/fink-buildlock-breseq-0.23-1_2014.08.02-03.18.21_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-breseq-0.23-1_2014.08.02-03.18.21_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-breseq-0.23-1. (Reading database ... 12825 files and directories currently installed.) Unpacking fink-buildlock-breseq-0.23-1 (from .../fink-buildlock-breseq-0.23-1_2014.08.02-03.18.21_darwin-x86_64.deb) ... Setting up fink-buildlock-breseq-0.23-1 (2014.08.02-03.18.21) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.Xo_l3 env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/breseq-0.23.tar.gz breseq-0.23/ breseq-0.23/aclocal.m4 breseq-0.23/AUTHORS breseq-0.23/aux_build/ breseq-0.23/._ChangeLog breseq-0.23/ChangeLog breseq-0.23/._configure breseq-0.23/configure breseq-0.23/._configure.ac breseq-0.23/configure.ac breseq-0.23/COPYING breseq-0.23/documentation/ breseq-0.23/extern/ breseq-0.23/INSTALL breseq-0.23/._Makefile.am breseq-0.23/Makefile.am breseq-0.23/Makefile.in breseq-0.23/NEWS breseq-0.23/._README breseq-0.23/README breseq-0.23/src/ breseq-0.23/tests/ breseq-0.23/tests/._common.sh breseq-0.23/tests/common.sh breseq-0.23/tests/data/ breseq-0.23/tests/lambda_mult_ref_read/ breseq-0.23/tests/test.sh breseq-0.23/tests/lambda_mult_ref_read/expected.gd breseq-0.23/tests/lambda_mult_ref_read/._testcmd.sh breseq-0.23/tests/lambda_mult_ref_read/testcmd.sh breseq-0.23/tests/data/lambda/ breseq-0.23/tests/data/lambda/._lambda.1-2.gbk breseq-0.23/tests/data/lambda/lambda.1-2.gbk breseq-0.23/tests/data/lambda/lambda.3.gbk breseq-0.23/tests/data/lambda/lambda.4.gbk breseq-0.23/tests/data/lambda/lambda.5.gbk breseq-0.23/tests/data/lambda/lambda_mixed_population.1.fastq breseq-0.23/tests/data/lambda/lambda_mixed_population.2.fastq breseq-0.23/tests/data/lambda/lambda_mixed_population.3.fastq breseq-0.23/tests/data/lambda/lambda_mixed_population.4.fastq breseq-0.23/tests/data/lambda/lambda_mixed_population.5.fastq breseq-0.23/src/c/ breseq-0.23/src/perl/ breseq-0.23/src/perl/GenomeDiff/ breseq-0.23/src/perl/GenomeDiff/bin/ breseq-0.23/src/perl/GenomeDiff/Build.PL breseq-0.23/src/perl/GenomeDiff/Changes breseq-0.23/src/perl/GenomeDiff/lib/ breseq-0.23/src/perl/GenomeDiff/Makefile.PL breseq-0.23/src/perl/GenomeDiff/MANIFEST breseq-0.23/src/perl/GenomeDiff/META.yml breseq-0.23/src/perl/GenomeDiff/README breseq-0.23/src/perl/GenomeDiff/t/ breseq-0.23/src/perl/GenomeDiff/t/00-load.t breseq-0.23/src/perl/GenomeDiff/t/manifest.t breseq-0.23/src/perl/GenomeDiff/t/pod-coverage.t breseq-0.23/src/perl/GenomeDiff/t/pod.t breseq-0.23/src/perl/GenomeDiff/lib/GenomeDiff/ breseq-0.23/src/perl/GenomeDiff/lib/GenomeDiff.pm breseq-0.23/src/perl/GenomeDiff/lib/GenomeDiff/BaseSubstitutionFile.pm breseq-0.23/src/perl/GenomeDiff/lib/GenomeDiff/Output.pm breseq-0.23/src/perl/GenomeDiff/lib/GenomeDiff/PreterminationTables.pm breseq-0.23/src/perl/GenomeDiff/lib/GenomeDiff/ReferenceSequence.pm breseq-0.23/src/perl/GenomeDiff/lib/GenomeDiff/SynonymousNonsynonymous.pm breseq-0.23/src/perl/GenomeDiff/bin/genomediff breseq-0.23/src/perl/GenomeDiff/bin/tree_utils breseq-0.23/src/c/breseq/ breseq-0.23/src/c/breseq/._alignment.cpp breseq-0.23/src/c/breseq/alignment.cpp breseq-0.23/src/c/breseq/._alignment_output.cpp breseq-0.23/src/c/breseq/alignment_output.cpp breseq-0.23/src/c/breseq/._anyoption.cpp breseq-0.23/src/c/breseq/anyoption.cpp breseq-0.23/src/c/breseq/breseq.png breseq-0.23/src/c/breseq/._breseq_cmdline.cpp breseq-0.23/src/c/breseq/breseq_cmdline.cpp breseq-0.23/src/c/breseq/breseq_small.png breseq-0.23/src/c/breseq/._calculate_trims.cpp breseq-0.23/src/c/breseq/calculate_trims.cpp breseq-0.23/src/c/breseq/._candidate_junctions.cpp breseq-0.23/src/c/breseq/candidate_junctions.cpp breseq-0.23/src/c/breseq/chisquare.cpp breseq-0.23/src/c/breseq/combined_circos.conf breseq-0.23/src/c/breseq/._contingency_loci.cpp breseq-0.23/src/c/breseq/contingency_loci.cpp breseq-0.23/src/c/breseq/coverage_distribution.cpp breseq-0.23/src/c/breseq/._coverage_distribution.r breseq-0.23/src/c/breseq/coverage_distribution.r breseq-0.23/src/c/breseq/._coverage_output.cpp breseq-0.23/src/c/breseq/coverage_output.cpp breseq-0.23/src/c/breseq/._error_count.cpp breseq-0.23/src/c/breseq/error_count.cpp breseq-0.23/src/c/breseq/._fasta.cpp breseq-0.23/src/c/breseq/fasta.cpp breseq-0.23/src/c/breseq/._fastq.cpp breseq-0.23/src/c/breseq/fastq.cpp breseq-0.23/src/c/breseq/._gdtools_cmdline.cpp breseq-0.23/src/c/breseq/gdtools_cmdline.cpp breseq-0.23/src/c/breseq/._genome_diff.cpp breseq-0.23/src/c/breseq/genome_diff.cpp breseq-0.23/src/c/breseq/._identify_mutations.cpp breseq-0.23/src/c/breseq/identify_mutations.cpp breseq-0.23/src/c/breseq/ideogram.conf breseq-0.23/src/c/breseq/indels.conf breseq-0.23/src/c/breseq/karyotype.and.layout.conf breseq-0.23/src/c/breseq/libbreseq/ breseq-0.23/src/c/breseq/._Makefile.am breseq-0.23/src/c/breseq/Makefile.am breseq-0.23/src/c/breseq/Makefile.in breseq-0.23/src/c/breseq/._mobs.conf breseq-0.23/src/c/breseq/mobs.conf breseq-0.23/src/c/breseq/._mutation_predictor.cpp breseq-0.23/src/c/breseq/mutation_predictor.cpp breseq-0.23/src/c/breseq/mutations.conf breseq-0.23/src/c/breseq/._output.cpp breseq-0.23/src/c/breseq/output.cpp breseq-0.23/src/c/breseq/._pileup.cpp breseq-0.23/src/c/breseq/pileup.cpp breseq-0.23/src/c/breseq/._pileup_base.cpp breseq-0.23/src/c/breseq/pileup_base.cpp breseq-0.23/src/c/breseq/._plot_coverage.r breseq-0.23/src/c/breseq/plot_coverage.r breseq-0.23/src/c/breseq/._plot_error_rate.r breseq-0.23/src/c/breseq/plot_error_rate.r breseq-0.23/src/c/breseq/._plot_jc_scores.r breseq-0.23/src/c/breseq/plot_jc_scores.r breseq-0.23/src/c/breseq/._polymorphism_statistics.r breseq-0.23/src/c/breseq/polymorphism_statistics.r breseq-0.23/src/c/breseq/._reference_sequence.cpp breseq-0.23/src/c/breseq/reference_sequence.cpp breseq-0.23/src/c/breseq/._resolve_alignments.cpp breseq-0.23/src/c/breseq/resolve_alignments.cpp breseq-0.23/src/c/breseq/._rna_seq.cpp breseq-0.23/src/c/breseq/rna_seq.cpp breseq-0.23/src/c/breseq/run_circos.sh breseq-0.23/src/c/breseq/._settings.cpp breseq-0.23/src/c/breseq/settings.cpp breseq-0.23/src/c/breseq/._summary.cpp breseq-0.23/src/c/breseq/summary.cpp breseq-0.23/src/c/breseq/libbreseq/._alignment.h breseq-0.23/src/c/breseq/libbreseq/alignment.h breseq-0.23/src/c/breseq/libbreseq/._alignment_output.h breseq-0.23/src/c/breseq/libbreseq/alignment_output.h breseq-0.23/src/c/breseq/libbreseq/._anyoption.h breseq-0.23/src/c/breseq/libbreseq/anyoption.h breseq-0.23/src/c/breseq/libbreseq/._calculate_trims.h breseq-0.23/src/c/breseq/libbreseq/calculate_trims.h breseq-0.23/src/c/breseq/libbreseq/._candidate_junctions.h breseq-0.23/src/c/breseq/libbreseq/candidate_junctions.h breseq-0.23/src/c/breseq/libbreseq/chisquare.h breseq-0.23/src/c/breseq/libbreseq/._common.h breseq-0.23/src/c/breseq/libbreseq/common.h breseq-0.23/src/c/breseq/libbreseq/._contingency_loci.h breseq-0.23/src/c/breseq/libbreseq/contingency_loci.h breseq-0.23/src/c/breseq/libbreseq/coverage_distribution.h breseq-0.23/src/c/breseq/libbreseq/._coverage_output.h breseq-0.23/src/c/breseq/libbreseq/coverage_output.h breseq-0.23/src/c/breseq/libbreseq/._error_count.h breseq-0.23/src/c/breseq/libbreseq/error_count.h breseq-0.23/src/c/breseq/libbreseq/._fasta.h breseq-0.23/src/c/breseq/libbreseq/fasta.h breseq-0.23/src/c/breseq/libbreseq/._fastq.h breseq-0.23/src/c/breseq/libbreseq/fastq.h breseq-0.23/src/c/breseq/libbreseq/._genome_diff.h breseq-0.23/src/c/breseq/libbreseq/genome_diff.h breseq-0.23/src/c/breseq/libbreseq/._identify_mutations.h breseq-0.23/src/c/breseq/libbreseq/identify_mutations.h breseq-0.23/src/c/breseq/libbreseq/._mutation_predictor.h breseq-0.23/src/c/breseq/libbreseq/mutation_predictor.h breseq-0.23/src/c/breseq/libbreseq/._output.h breseq-0.23/src/c/breseq/libbreseq/output.h breseq-0.23/src/c/breseq/libbreseq/._pileup.h breseq-0.23/src/c/breseq/libbreseq/pileup.h breseq-0.23/src/c/breseq/libbreseq/._pileup_base.h breseq-0.23/src/c/breseq/libbreseq/pileup_base.h breseq-0.23/src/c/breseq/libbreseq/._reference_sequence.h breseq-0.23/src/c/breseq/libbreseq/reference_sequence.h breseq-0.23/src/c/breseq/libbreseq/._resolve_alignments.h breseq-0.23/src/c/breseq/libbreseq/resolve_alignments.h breseq-0.23/src/c/breseq/libbreseq/._rna_seq.h breseq-0.23/src/c/breseq/libbreseq/rna_seq.h breseq-0.23/src/c/breseq/libbreseq/._settings.h breseq-0.23/src/c/breseq/libbreseq/settings.h breseq-0.23/src/c/breseq/libbreseq/._storable.h breseq-0.23/src/c/breseq/libbreseq/storable.h breseq-0.23/src/c/breseq/libbreseq/._summary.h breseq-0.23/src/c/breseq/libbreseq/summary.h breseq-0.23/extern/samtools-0.1.18/ breseq-0.23/extern/._samtools_modifications.txt breseq-0.23/extern/samtools_modifications.txt breseq-0.23/extern/samtools-0.1.18/._AUTHORS breseq-0.23/extern/samtools-0.1.18/AUTHORS breseq-0.23/extern/samtools-0.1.18/._bam.c breseq-0.23/extern/samtools-0.1.18/bam.c breseq-0.23/extern/samtools-0.1.18/._bam.h breseq-0.23/extern/samtools-0.1.18/bam.h breseq-0.23/extern/samtools-0.1.18/._bam2bcf.c breseq-0.23/extern/samtools-0.1.18/bam2bcf.c breseq-0.23/extern/samtools-0.1.18/._bam2bcf.h breseq-0.23/extern/samtools-0.1.18/bam2bcf.h breseq-0.23/extern/samtools-0.1.18/._bam2bcf_indel.c breseq-0.23/extern/samtools-0.1.18/bam2bcf_indel.c breseq-0.23/extern/samtools-0.1.18/._bam2depth.c breseq-0.23/extern/samtools-0.1.18/bam2depth.c breseq-0.23/extern/samtools-0.1.18/._bam_aux.c breseq-0.23/extern/samtools-0.1.18/bam_aux.c breseq-0.23/extern/samtools-0.1.18/._bam_cat.c breseq-0.23/extern/samtools-0.1.18/bam_cat.c breseq-0.23/extern/samtools-0.1.18/._bam_color.c breseq-0.23/extern/samtools-0.1.18/bam_color.c breseq-0.23/extern/samtools-0.1.18/._bam_endian.h breseq-0.23/extern/samtools-0.1.18/bam_endian.h breseq-0.23/extern/samtools-0.1.18/._bam_import.c breseq-0.23/extern/samtools-0.1.18/bam_import.c breseq-0.23/extern/samtools-0.1.18/._bam_index.c breseq-0.23/extern/samtools-0.1.18/bam_index.c breseq-0.23/extern/samtools-0.1.18/._bam_lpileup.c breseq-0.23/extern/samtools-0.1.18/bam_lpileup.c breseq-0.23/extern/samtools-0.1.18/._bam_mate.c breseq-0.23/extern/samtools-0.1.18/bam_mate.c breseq-0.23/extern/samtools-0.1.18/._bam_md.c breseq-0.23/extern/samtools-0.1.18/bam_md.c breseq-0.23/extern/samtools-0.1.18/._bam_pileup.c breseq-0.23/extern/samtools-0.1.18/bam_pileup.c breseq-0.23/extern/samtools-0.1.18/bam_plcmd.c breseq-0.23/extern/samtools-0.1.18/._bam_reheader.c breseq-0.23/extern/samtools-0.1.18/bam_reheader.c breseq-0.23/extern/samtools-0.1.18/._bam_rmdup.c breseq-0.23/extern/samtools-0.1.18/bam_rmdup.c breseq-0.23/extern/samtools-0.1.18/._bam_rmdupse.c breseq-0.23/extern/samtools-0.1.18/bam_rmdupse.c breseq-0.23/extern/samtools-0.1.18/._bam_sort.c breseq-0.23/extern/samtools-0.1.18/bam_sort.c breseq-0.23/extern/samtools-0.1.18/._bam_stat.c breseq-0.23/extern/samtools-0.1.18/bam_stat.c breseq-0.23/extern/samtools-0.1.18/._bam_tview.c breseq-0.23/extern/samtools-0.1.18/bam_tview.c breseq-0.23/extern/samtools-0.1.18/._bamtk.c breseq-0.23/extern/samtools-0.1.18/bamtk.c breseq-0.23/extern/samtools-0.1.18/bcftools/ breseq-0.23/extern/samtools-0.1.18/._bedidx.c breseq-0.23/extern/samtools-0.1.18/bedidx.c breseq-0.23/extern/samtools-0.1.18/._bgzf.c breseq-0.23/extern/samtools-0.1.18/bgzf.c breseq-0.23/extern/samtools-0.1.18/._bgzf.h breseq-0.23/extern/samtools-0.1.18/bgzf.h breseq-0.23/extern/samtools-0.1.18/._bgzip.c breseq-0.23/extern/samtools-0.1.18/bgzip.c breseq-0.23/extern/samtools-0.1.18/ChangeLog breseq-0.23/extern/samtools-0.1.18/._COPYING breseq-0.23/extern/samtools-0.1.18/COPYING breseq-0.23/extern/samtools-0.1.18/._cut_target.c breseq-0.23/extern/samtools-0.1.18/cut_target.c breseq-0.23/extern/samtools-0.1.18/._errmod.c breseq-0.23/extern/samtools-0.1.18/errmod.c breseq-0.23/extern/samtools-0.1.18/._errmod.h breseq-0.23/extern/samtools-0.1.18/errmod.h breseq-0.23/extern/samtools-0.1.18/examples/ breseq-0.23/extern/samtools-0.1.18/._faidx.c breseq-0.23/extern/samtools-0.1.18/faidx.c breseq-0.23/extern/samtools-0.1.18/._faidx.h breseq-0.23/extern/samtools-0.1.18/faidx.h breseq-0.23/extern/samtools-0.1.18/._INSTALL breseq-0.23/extern/samtools-0.1.18/INSTALL breseq-0.23/extern/samtools-0.1.18/._kaln.c breseq-0.23/extern/samtools-0.1.18/kaln.c breseq-0.23/extern/samtools-0.1.18/._kaln.h breseq-0.23/extern/samtools-0.1.18/kaln.h breseq-0.23/extern/samtools-0.1.18/._khash.h breseq-0.23/extern/samtools-0.1.18/khash.h breseq-0.23/extern/samtools-0.1.18/._klist.h breseq-0.23/extern/samtools-0.1.18/klist.h breseq-0.23/extern/samtools-0.1.18/._knetfile.c breseq-0.23/extern/samtools-0.1.18/knetfile.c breseq-0.23/extern/samtools-0.1.18/._knetfile.h breseq-0.23/extern/samtools-0.1.18/knetfile.h breseq-0.23/extern/samtools-0.1.18/._kprobaln.c breseq-0.23/extern/samtools-0.1.18/kprobaln.c breseq-0.23/extern/samtools-0.1.18/._kprobaln.h breseq-0.23/extern/samtools-0.1.18/kprobaln.h breseq-0.23/extern/samtools-0.1.18/._kseq.h breseq-0.23/extern/samtools-0.1.18/kseq.h breseq-0.23/extern/samtools-0.1.18/._ksort.h breseq-0.23/extern/samtools-0.1.18/ksort.h breseq-0.23/extern/samtools-0.1.18/._kstring.c breseq-0.23/extern/samtools-0.1.18/kstring.c 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breseq-0.23/extern/samtools-0.1.18/sam.h breseq-0.23/extern/samtools-0.1.18/._sam_header.c breseq-0.23/extern/samtools-0.1.18/sam_header.c breseq-0.23/extern/samtools-0.1.18/._sam_header.h breseq-0.23/extern/samtools-0.1.18/sam_header.h breseq-0.23/extern/samtools-0.1.18/._sam_view.c breseq-0.23/extern/samtools-0.1.18/sam_view.c breseq-0.23/extern/samtools-0.1.18/._sample.c breseq-0.23/extern/samtools-0.1.18/sample.c breseq-0.23/extern/samtools-0.1.18/._sample.h breseq-0.23/extern/samtools-0.1.18/sample.h breseq-0.23/extern/samtools-0.1.18/._samtools.1 breseq-0.23/extern/samtools-0.1.18/samtools.1 breseq-0.23/extern/samtools-0.1.18/win32/ breseq-0.23/extern/samtools-0.1.18/win32/._xcurses.h breseq-0.23/extern/samtools-0.1.18/win32/xcurses.h breseq-0.23/extern/samtools-0.1.18/win32/._zconf.h breseq-0.23/extern/samtools-0.1.18/win32/zconf.h breseq-0.23/extern/samtools-0.1.18/win32/._zlib.h breseq-0.23/extern/samtools-0.1.18/win32/zlib.h breseq-0.23/extern/samtools-0.1.18/misc/._blast2sam.pl breseq-0.23/extern/samtools-0.1.18/misc/blast2sam.pl breseq-0.23/extern/samtools-0.1.18/misc/._bowtie2sam.pl breseq-0.23/extern/samtools-0.1.18/misc/bowtie2sam.pl breseq-0.23/extern/samtools-0.1.18/misc/._export2sam.pl breseq-0.23/extern/samtools-0.1.18/misc/export2sam.pl breseq-0.23/extern/samtools-0.1.18/misc/._HmmGlocal.java breseq-0.23/extern/samtools-0.1.18/misc/HmmGlocal.java breseq-0.23/extern/samtools-0.1.18/misc/._interpolate_sam.pl breseq-0.23/extern/samtools-0.1.18/misc/interpolate_sam.pl breseq-0.23/extern/samtools-0.1.18/misc/._Makefile breseq-0.23/extern/samtools-0.1.18/misc/Makefile breseq-0.23/extern/samtools-0.1.18/misc/._maq2sam.c breseq-0.23/extern/samtools-0.1.18/misc/maq2sam.c breseq-0.23/extern/samtools-0.1.18/misc/._md5.c breseq-0.23/extern/samtools-0.1.18/misc/md5.c breseq-0.23/extern/samtools-0.1.18/misc/._md5.h breseq-0.23/extern/samtools-0.1.18/misc/md5.h breseq-0.23/extern/samtools-0.1.18/misc/._md5fa.c 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breseq-0.23/extern/samtools-0.1.18/misc/._zoom2sam.pl breseq-0.23/extern/samtools-0.1.18/misc/zoom2sam.pl breseq-0.23/extern/samtools-0.1.18/examples/._00README.txt breseq-0.23/extern/samtools-0.1.18/examples/00README.txt breseq-0.23/extern/samtools-0.1.18/examples/._bam2bed.c breseq-0.23/extern/samtools-0.1.18/examples/bam2bed.c breseq-0.23/extern/samtools-0.1.18/examples/._calDepth.c breseq-0.23/extern/samtools-0.1.18/examples/calDepth.c breseq-0.23/extern/samtools-0.1.18/examples/._ex1.fa breseq-0.23/extern/samtools-0.1.18/examples/ex1.fa breseq-0.23/extern/samtools-0.1.18/examples/._ex1.sam.gz breseq-0.23/extern/samtools-0.1.18/examples/ex1.sam.gz breseq-0.23/extern/samtools-0.1.18/examples/._Makefile breseq-0.23/extern/samtools-0.1.18/examples/Makefile breseq-0.23/extern/samtools-0.1.18/examples/._toy.fa breseq-0.23/extern/samtools-0.1.18/examples/toy.fa breseq-0.23/extern/samtools-0.1.18/examples/._toy.sam breseq-0.23/extern/samtools-0.1.18/examples/toy.sam breseq-0.23/extern/samtools-0.1.18/bcftools/._bcf.c breseq-0.23/extern/samtools-0.1.18/bcftools/bcf.c breseq-0.23/extern/samtools-0.1.18/bcftools/bcf.h breseq-0.23/extern/samtools-0.1.18/bcftools/._bcf.tex breseq-0.23/extern/samtools-0.1.18/bcftools/bcf.tex breseq-0.23/extern/samtools-0.1.18/bcftools/._bcf2qcall.c breseq-0.23/extern/samtools-0.1.18/bcftools/bcf2qcall.c breseq-0.23/extern/samtools-0.1.18/bcftools/._bcfutils.c breseq-0.23/extern/samtools-0.1.18/bcftools/bcfutils.c breseq-0.23/extern/samtools-0.1.18/bcftools/call1.c breseq-0.23/extern/samtools-0.1.18/bcftools/._em.c breseq-0.23/extern/samtools-0.1.18/bcftools/em.c breseq-0.23/extern/samtools-0.1.18/bcftools/fet.c breseq-0.23/extern/samtools-0.1.18/bcftools/._index.c breseq-0.23/extern/samtools-0.1.18/bcftools/index.c breseq-0.23/extern/samtools-0.1.18/bcftools/._kfunc.c breseq-0.23/extern/samtools-0.1.18/bcftools/kfunc.c breseq-0.23/extern/samtools-0.1.18/bcftools/._kmin.c 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breseq-0.23/extern/samtools-0.1.18/bcftools/vcf.c breseq-0.23/extern/samtools-0.1.18/bcftools/._vcfutils.pl breseq-0.23/extern/samtools-0.1.18/bcftools/vcfutils.pl breseq-0.23/documentation/_images/ breseq-0.23/documentation/_sources/ breseq-0.23/documentation/_static/ breseq-0.23/documentation/acknowledgments.html breseq-0.23/documentation/gd_format.html breseq-0.23/documentation/gd_usage.html breseq-0.23/documentation/genindex.html breseq-0.23/documentation/index.html breseq-0.23/documentation/installation.html breseq-0.23/documentation/introduction.html breseq-0.23/documentation/methods.html breseq-0.23/documentation/objects.inv breseq-0.23/documentation/output.html breseq-0.23/documentation/references.html breseq-0.23/documentation/search.html breseq-0.23/documentation/searchindex.js breseq-0.23/documentation/test_drive.html breseq-0.23/documentation/usage.html breseq-0.23/documentation/_static/ajax-loader.gif breseq-0.23/documentation/_static/basic.css 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breseq-0.23/documentation/_sources/gd_usage.txt breseq-0.23/documentation/_sources/index.txt breseq-0.23/documentation/_sources/installation.txt breseq-0.23/documentation/_sources/introduction.txt breseq-0.23/documentation/_sources/methods.txt breseq-0.23/documentation/_sources/output.txt breseq-0.23/documentation/_sources/references.txt breseq-0.23/documentation/_sources/test_drive.txt breseq-0.23/documentation/_sources/usage.txt breseq-0.23/documentation/_images/amp_1.png breseq-0.23/documentation/_images/coverage_distribution.png breseq-0.23/documentation/_images/del_1.png breseq-0.23/documentation/_images/del_2.png breseq-0.23/documentation/_images/end_trimming_example.png breseq-0.23/documentation/_images/error_rates.png breseq-0.23/documentation/_images/ins_1.png breseq-0.23/documentation/_images/ins_2.png breseq-0.23/documentation/_images/jc_1.png breseq-0.23/documentation/_images/jc_2.png breseq-0.23/documentation/_images/math/ breseq-0.23/documentation/_images/mc_1.png breseq-0.23/documentation/_images/missed_mutation_no_trimming.png breseq-0.23/documentation/_images/mob_1.png breseq-0.23/documentation/_images/mob_2.png breseq-0.23/documentation/_images/mob_3.png breseq-0.23/documentation/_images/ra_1.png breseq-0.23/documentation/_images/region_coverage_example.png breseq-0.23/documentation/_images/snp_1.png breseq-0.23/documentation/_images/snp_2.png breseq-0.23/documentation/_images/sub_1.png breseq-0.23/documentation/_images/math/2eefa663f8b77523a220eb85286f5440109ca3f7.png breseq-0.23/documentation/_images/math/57b7923f53dc375a1d79fd1ff7a62813eadc7300.png breseq-0.23/documentation/_images/math/d577021c1b98dad39e379547de48f52d7d50d7ee.png breseq-0.23/aux_build/compile breseq-0.23/aux_build/config.guess breseq-0.23/aux_build/config.h.in breseq-0.23/aux_build/config.sub breseq-0.23/aux_build/depcomp breseq-0.23/aux_build/install-sh breseq-0.23/aux_build/ltmain.sh breseq-0.23/aux_build/m4/ breseq-0.23/aux_build/missing breseq-0.23/aux_build/m4/libtool.m4 breseq-0.23/aux_build/m4/ltoptions.m4 breseq-0.23/aux_build/m4/ltsugar.m4 breseq-0.23/aux_build/m4/ltversion.m4 breseq-0.23/aux_build/m4/lt~obsolete.m4 sudo -u fink-bld [ENV] sh -c /tmp/fink.LBhxi ./configure --prefix=/sw --enable-dependency-tracking --disable-static --prefix=/sw/lib/breseq checking build system type... x86_64-apple-darwin13.3.0 checking host system type... x86_64-apple-darwin13.3.0 checking how to print strings... printf checking for gcc... gcc-fsf-4.8 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc-fsf-4.8 accepts -g... yes checking for gcc-fsf-4.8 option to accept ISO C89... none needed checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc-fsf-4.8... /usr/bin/ld checking if the linker (/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 how to convert x86_64-apple-darwin13.3.0 file names to x86_64-apple-darwin13.3.0 format... func_convert_file_noop checking how to convert x86_64-apple-darwin13.3.0 file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... no checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... no checking for strip... strip checking for ranlib... ranlib checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking command to parse /usr/bin/nm output from gcc-fsf-4.8 object... ok checking for sysroot... no checking for mt... no checking if : is a manifest tool... no 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 -force_load linker flag... yes checking how to run the C preprocessor... gcc-fsf-4.8 -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc-fsf-4.8 supports -fno-rtti -fno-exceptions... no checking for gcc-fsf-4.8 option to produce PIC... -fno-common -DPIC checking if gcc-fsf-4.8 PIC flag -fno-common -DPIC works... yes checking if gcc-fsf-4.8 static flag -static works... no checking if gcc-fsf-4.8 supports -c -o file.o... yes checking if gcc-fsf-4.8 supports -c -o file.o... (cached) yes checking whether the gcc-fsf-4.8 linker (/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 whether build environment is sane... yes checking for a thread-safe mkdir -p... aux_build/install-sh -c -d checking whether make sets $(MAKE)... yes checking for style of include used by make... GNU checking dependency style of gcc-fsf-4.8... gcc3 checking whether gcc-fsf-4.8 and cc understand -c and -o together... yes checking whether we are using the GNU C++ compiler... yes checking whether g++-fsf-4.8 accepts -g... yes checking how to run the C++ preprocessor... g++-fsf-4.8 -E checking for ld used by g++-fsf-4.8... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... no checking whether the g++-fsf-4.8 linker (/usr/bin/ld) supports shared libraries... yes checking for g++-fsf-4.8 option to produce PIC... -fno-common -DPIC checking if g++-fsf-4.8 PIC flag -fno-common -DPIC works... yes checking if g++-fsf-4.8 static flag -static works... no checking if g++-fsf-4.8 supports -c -o file.o... yes checking if g++-fsf-4.8 supports -c -o file.o... (cached) yes checking whether the g++-fsf-4.8 linker (/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 dependency style of g++-fsf-4.8... gcc3 checking for gawk... (cached) awk checking how to run the C preprocessor... gcc-fsf-4.8 -E checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking arpa/inet.h usability... yes checking arpa/inet.h presence... yes checking for arpa/inet.h... yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking for inttypes.h... (cached) yes checking netdb.h usability... yes checking netdb.h presence... yes checking for netdb.h... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdint.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking sys/socket.h usability... yes checking sys/socket.h presence... yes checking for sys/socket.h... yes checking for unistd.h... (cached) yes checking wchar.h usability... yes checking wchar.h presence... yes checking for wchar.h... yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for inline... inline checking for int16_t... yes checking for int32_t... yes checking for int64_t... yes checking for int8_t... yes checking for off_t... yes checking for size_t... yes checking for uint16_t... yes checking for uint32_t... yes checking for uint64_t... yes checking for uint8_t... yes checking for _LARGEFILE_SOURCE value needed for large files... no checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for bzero... yes checking for gethostbyaddr... yes checking for gethostbyname... yes checking for memmove... yes checking for memset... yes checking for pow... yes checking for select... yes checking for socket... yes checking for sqrt... yes checking for strchr... yes checking for strdup... yes checking for strerror... yes checking for strstr... yes checking for strtol... yes checking for ftello... yes checking for library containing wclear... -lcurses checking for library containing deflateSetHeader... -lz checking for library containing acosf... none required checking for .hg/branchheads.cache... no checking for .hg/cache/branchheads... no checking for .hg/branchheads.cache... (cached) no checking for .hg/cache/branchheads... (cached) no configure: Detected host 'darwin'. checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating extern/samtools-0.1.18/bcftools/Makefile config.status: creating extern/samtools-0.1.18/Makefile config.status: creating src/c/breseq/Makefile config.status: creating Makefile config.status: creating aux_build/config.h config.status: executing libtool commands config.status: executing depfiles commands make Making all in extern/samtools-0.1.18 Making all in bcftools /bin/sh ../../../libtool --tag=CC --mode=compile gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../../aux_build -I/sw/include -I../../../extern/samtools-0.1.18 -g -O2 -MT libbcf_la-bcf.lo -MD -MP -MF .deps/libbcf_la-bcf.Tpo -c -o libbcf_la-bcf.lo `test -f 'bcf.c' || echo './'`bcf.c /bin/sh ../../../libtool --tag=CC --mode=compile gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../../aux_build -I/sw/include -I../../../extern/samtools-0.1.18 -g -O2 -MT libbcf_la-bcf2qcall.lo -MD 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.deps/reference_sequence.Tpo -c -o reference_sequence.lo reference_sequence.cpp libtool: compile: g++-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../../aux_build -I../../../extern/samtools-0.1.18 -I../../../aux_build -DDATADIR=\"/sw/lib/breseq/share/breseq\" -I/sw/include -g -O2 -MT reference_sequence.lo -MD -MP -MF .deps/reference_sequence.Tpo -c reference_sequence.cpp -fno-common -DPIC -o .libs/reference_sequence.o mv -f .deps/fastq.Tpo .deps/fastq.Plo /bin/sh ../../../libtool --tag=CXX --mode=compile g++-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../../aux_build -I../../../extern/samtools-0.1.18 -I../../../aux_build -DDATADIR=\"/sw/lib/breseq/share/breseq\" -I/sw/include -g -O2 -MT resolve_alignments.lo -MD -MP -MF .deps/resolve_alignments.Tpo -c -o resolve_alignments.lo resolve_alignments.cpp libtool: compile: g++-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../../aux_build -I../../../extern/samtools-0.1.18 -I../../../aux_build -DDATADIR=\"/sw/lib/breseq/share/breseq\" -I/sw/include -g -O2 -MT resolve_alignments.lo -MD -MP -MF .deps/resolve_alignments.Tpo -c resolve_alignments.cpp -fno-common -DPIC -o .libs/resolve_alignments.o mv -f .deps/pileup.Tpo .deps/pileup.Plo /bin/sh ../../../libtool --tag=CXX --mode=compile g++-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../../aux_build -I../../../extern/samtools-0.1.18 -I../../../aux_build -DDATADIR=\"/sw/lib/breseq/share/breseq\" -I/sw/include -g -O2 -MT rna_seq.lo -MD -MP -MF .deps/rna_seq.Tpo -c -o rna_seq.lo rna_seq.cpp libtool: compile: g++-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../../aux_build -I../../../extern/samtools-0.1.18 -I../../../aux_build -DDATADIR=\"/sw/lib/breseq/share/breseq\" -I/sw/include -g -O2 -MT rna_seq.lo -MD -MP -MF .deps/rna_seq.Tpo -c rna_seq.cpp -fno-common -DPIC -o .libs/rna_seq.o mv -f .deps/identify_mutations.Tpo .deps/identify_mutations.Plo /bin/sh ../../../libtool --tag=CXX --mode=compile g++-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../../aux_build -I../../../extern/samtools-0.1.18 -I../../../aux_build -DDATADIR=\"/sw/lib/breseq/share/breseq\" -I/sw/include -g -O2 -MT settings.lo -MD -MP -MF .deps/settings.Tpo -c -o settings.lo settings.cpp libtool: compile: g++-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../../aux_build -I../../../extern/samtools-0.1.18 -I../../../aux_build -DDATADIR=\"/sw/lib/breseq/share/breseq\" -I/sw/include -g -O2 -MT settings.lo -MD -MP -MF .deps/settings.Tpo -c settings.cpp -fno-common -DPIC -o .libs/settings.o mv -f .deps/pileup_base.Tpo .deps/pileup_base.Plo /bin/sh ../../../libtool --tag=CXX --mode=compile g++-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../../aux_build -I../../../extern/samtools-0.1.18 -I../../../aux_build -DDATADIR=\"/sw/lib/breseq/share/breseq\" -I/sw/include -g -O2 -MT summary.lo -MD -MP -MF .deps/summary.Tpo -c -o summary.lo summary.cpp libtool: compile: g++-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../../aux_build -I../../../extern/samtools-0.1.18 -I../../../aux_build -DDATADIR=\"/sw/lib/breseq/share/breseq\" -I/sw/include -g -O2 -MT summary.lo -MD -MP -MF .deps/summary.Tpo -c summary.cpp -fno-common -DPIC -o .libs/summary.o mv -f .deps/summary.Tpo .deps/summary.Plo g++-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../../aux_build -I../../../extern/samtools-0.1.18 -I../../../aux_build -DDATADIR=\"/sw/lib/breseq/share/breseq\" -I/sw/include -g -O2 -MT breseq_cmdline.o -MD -MP -MF .deps/breseq_cmdline.Tpo -c -o breseq_cmdline.o breseq_cmdline.cpp mv -f .deps/rna_seq.Tpo .deps/rna_seq.Plo g++-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../../aux_build -I../../../extern/samtools-0.1.18 -I../../../aux_build -DDATADIR=\"/sw/lib/breseq/share/breseq\" -I/sw/include -g -O2 -MT gdtools_cmdline.o -MD -MP -MF .deps/gdtools_cmdline.Tpo -c -o gdtools_cmdline.o gdtools_cmdline.cpp mv -f .deps/resolve_alignments.Tpo .deps/resolve_alignments.Plo mv -f .deps/settings.Tpo .deps/settings.Plo mv -f .deps/mutation_predictor.Tpo .deps/mutation_predictor.Plo mv -f .deps/reference_sequence.Tpo .deps/reference_sequence.Plo mv -f .deps/breseq_cmdline.Tpo .deps/breseq_cmdline.Po mv -f .deps/genome_diff.Tpo .deps/genome_diff.Plo mv -f .deps/gdtools_cmdline.Tpo .deps/gdtools_cmdline.Po mv -f .deps/output.Tpo .deps/output.Plo /bin/sh ../../../libtool --tag=CXX --mode=link g++-fsf-4.8 -g -O2 -static -L/sw/lib -o libbreseq.la alignment.lo alignment_output.lo anyoption.lo calculate_trims.lo candidate_junctions.lo chisquare.lo contingency_loci.lo coverage_output.lo coverage_distribution.lo error_count.lo fasta.lo fastq.lo genome_diff.lo identify_mutations.lo mutation_predictor.lo output.lo pileup.lo pileup_base.lo reference_sequence.lo resolve_alignments.lo rna_seq.lo settings.lo summary.lo ../../../extern/samtools-0.1.18/libbam.la libtool: link: (cd .libs/libbreseq.lax/libbam.a && ar x "/sw/build.build/breseq-0.23-1/breseq-0.23/src/c/breseq/../../../extern/samtools-0.1.18/.libs/libbam.a") libtool: link: ar cru .libs/libbreseq.a .libs/alignment.o .libs/alignment_output.o .libs/anyoption.o .libs/calculate_trims.o .libs/candidate_junctions.o .libs/chisquare.o .libs/contingency_loci.o .libs/coverage_output.o .libs/coverage_distribution.o .libs/error_count.o .libs/fasta.o .libs/fastq.o .libs/genome_diff.o .libs/identify_mutations.o .libs/mutation_predictor.o .libs/output.o .libs/pileup.o .libs/pileup_base.o .libs/reference_sequence.o .libs/resolve_alignments.o .libs/rna_seq.o .libs/settings.o .libs/summary.o .libs/libbreseq.lax/libbam.a/libbam_la-bam.o .libs/libbreseq.lax/libbam.a/libbam_la-bam2bcf_indel.o .libs/libbreseq.lax/libbam.a/libbam_la-bam2depth.o .libs/libbreseq.lax/libbam.a/libbam_la-bam_aux.o .libs/libbreseq.lax/libbam.a/libbam_la-bam_cat.o .libs/libbreseq.lax/libbam.a/libbam_la-bam_import.o .libs/libbreseq.lax/libbam.a/libbam_la-bam_index.o .libs/libbreseq.lax/libbam.a/libbam_la-bam_lpileup.o .libs/libbreseq.lax/libbam.a/libbam_la-bam_md.o .libs/libbreseq.lax/libbam.a/libbam_la-bam_pileup.o .libs/libbreseq.lax/libbam.a/libbam_la-bam_reheader.o .libs/libbreseq.lax/libbam.a/libbam_la-bam_sort.o .libs/libbreseq.lax/libbam.a/libbam_la-bedidx.o .libs/libbreseq.lax/libbam.a/libbam_la-bgzf.o .libs/libbreseq.lax/libbam.a/libbam_la-bgzip.o .libs/libbreseq.lax/libbam.a/libbam_la-faidx.o .libs/libbreseq.lax/libbam.a/libbam_la-knetfile.o .libs/libbreseq.lax/libbam.a/libbam_la-kprobaln.o .libs/libbreseq.lax/libbam.a/libbam_la-kstring.o .libs/libbreseq.lax/libbam.a/libbam_la-razf.o .libs/libbreseq.lax/libbam.a/libbam_la-razip.o .libs/libbreseq.lax/libbam.a/libbam_la-sam.o .libs/libbreseq.lax/libbam.a/libbam_la-sam_header.o libtool: link: ranlib .libs/libbreseq.a libtool: link: rm -fr .libs/libbreseq.lax libtool: link: ( cd ".libs" && rm -f "libbreseq.la" && ln -s "../libbreseq.la" "libbreseq.la" ) /bin/sh ../../../libtool --tag=CXX --mode=link g++-fsf-4.8 -g -O2 -static -L/sw/lib -o breseq breseq_cmdline.o ../../../extern/samtools-0.1.18/libbam.la libbreseq.la /bin/sh ../../../libtool --tag=CXX --mode=link g++-fsf-4.8 -g -O2 -static -L/sw/lib -o gdtools gdtools_cmdline.o ../../../extern/samtools-0.1.18/libbam.la libbreseq.la libtool: link: g++-fsf-4.8 -g -O2 -o breseq breseq_cmdline.o -L/sw/lib ../../../extern/samtools-0.1.18/.libs/libbam.a ./.libs/libbreseq.a -lz -lcurses libtool: link: g++-fsf-4.8 -g -O2 -o gdtools gdtools_cmdline.o -L/sw/lib ../../../extern/samtools-0.1.18/.libs/libbam.a ./.libs/libbreseq.a -lz -lcurses echo "export TESTBINPREFIX=/sw/build.build/breseq-0.23-1/breseq-0.23/src/c/breseq" > tests/test.config; echo "export BRESEQ_DATA_PATH=/sw/build.build/breseq-0.23-1/breseq-0.23/src/c/breseq" >> tests/test.config; echo "export BRESEQ_SAMTOOLS_PATH=/sw/build.build/breseq-0.23-1/breseq-0.23/extern/samtools-0.1.18" >> tests/test.config; fink-package-precedence . Scanning /\.Plo,\.Po$/ dependency files... ./extern/samtools-0.1.18/.deps/libbam_la-bam.Plo ./extern/samtools-0.1.18/.deps/libbam_la-bam2bcf_indel.Plo ./extern/samtools-0.1.18/.deps/libbam_la-bam2depth.Plo ./extern/samtools-0.1.18/.deps/libbam_la-bam_aux.Plo ./extern/samtools-0.1.18/.deps/libbam_la-bam_cat.Plo ./extern/samtools-0.1.18/.deps/libbam_la-bam_import.Plo ./extern/samtools-0.1.18/.deps/libbam_la-bam_index.Plo ./extern/samtools-0.1.18/.deps/libbam_la-bam_lpileup.Plo ./extern/samtools-0.1.18/.deps/libbam_la-bam_md.Plo ./extern/samtools-0.1.18/.deps/libbam_la-bam_pileup.Plo ./extern/samtools-0.1.18/.deps/libbam_la-bam_reheader.Plo ./extern/samtools-0.1.18/.deps/libbam_la-bam_sort.Plo ./extern/samtools-0.1.18/.deps/libbam_la-bedidx.Plo ./extern/samtools-0.1.18/.deps/libbam_la-bgzf.Plo ./extern/samtools-0.1.18/.deps/libbam_la-bgzip.Plo ./extern/samtools-0.1.18/.deps/libbam_la-faidx.Plo ./extern/samtools-0.1.18/.deps/libbam_la-knetfile.Plo ./extern/samtools-0.1.18/.deps/libbam_la-kprobaln.Plo ./extern/samtools-0.1.18/.deps/libbam_la-kstring.Plo ./extern/samtools-0.1.18/.deps/libbam_la-razf.Plo ./extern/samtools-0.1.18/.deps/libbam_la-razip.Plo ./extern/samtools-0.1.18/.deps/libbam_la-sam.Plo ./extern/samtools-0.1.18/.deps/libbam_la-sam_header.Plo ./extern/samtools-0.1.18/.deps/samtools-bam2bcf.Po ./extern/samtools-0.1.18/.deps/samtools-bam2bcf_indel.Po ./extern/samtools-0.1.18/.deps/samtools-bam_color.Po ./extern/samtools-0.1.18/.deps/samtools-bam_mate.Po ./extern/samtools-0.1.18/.deps/samtools-bam_plcmd.Po ./extern/samtools-0.1.18/.deps/samtools-bam_rmdup.Po ./extern/samtools-0.1.18/.deps/samtools-bam_rmdupse.Po ./extern/samtools-0.1.18/.deps/samtools-bam_stat.Po ./extern/samtools-0.1.18/.deps/samtools-bam_tview.Po ./extern/samtools-0.1.18/.deps/samtools-bamtk.Po ./extern/samtools-0.1.18/.deps/samtools-cut_target.Po ./extern/samtools-0.1.18/.deps/samtools-errmod.Po ./extern/samtools-0.1.18/.deps/samtools-kaln.Po ./extern/samtools-0.1.18/.deps/samtools-phase.Po ./extern/samtools-0.1.18/.deps/samtools-sam_view.Po ./extern/samtools-0.1.18/.deps/samtools-sample.Po ./extern/samtools-0.1.18/bcftools/.deps/bcftools-bedidx.Po ./extern/samtools-0.1.18/bcftools/.deps/bcftools-bgzf.Po ./extern/samtools-0.1.18/bcftools/.deps/bcftools-call1.Po ./extern/samtools-0.1.18/bcftools/.deps/bcftools-knetfile.Po ./extern/samtools-0.1.18/bcftools/.deps/bcftools-kstring.Po ./extern/samtools-0.1.18/bcftools/.deps/bcftools-main.Po ./extern/samtools-0.1.18/bcftools/.deps/libbcf_la-bcf.Plo ./extern/samtools-0.1.18/bcftools/.deps/libbcf_la-bcf2qcall.Plo ./extern/samtools-0.1.18/bcftools/.deps/libbcf_la-bcfutils.Plo ./extern/samtools-0.1.18/bcftools/.deps/libbcf_la-em.Plo ./extern/samtools-0.1.18/bcftools/.deps/libbcf_la-fet.Plo ./extern/samtools-0.1.18/bcftools/.deps/libbcf_la-index.Plo ./extern/samtools-0.1.18/bcftools/.deps/libbcf_la-kfunc.Plo ./extern/samtools-0.1.18/bcftools/.deps/libbcf_la-kmin.Plo ./extern/samtools-0.1.18/bcftools/.deps/libbcf_la-mut.Plo ./extern/samtools-0.1.18/bcftools/.deps/libbcf_la-prob1.Plo ./extern/samtools-0.1.18/bcftools/.deps/libbcf_la-vcf.Plo ./src/c/breseq/.deps/alignment.Plo ./src/c/breseq/.deps/alignment_output.Plo ./src/c/breseq/.deps/anyoption.Plo ./src/c/breseq/.deps/breseq_cmdline.Po ./src/c/breseq/.deps/calculate_trims.Plo ./src/c/breseq/.deps/candidate_junctions.Plo ./src/c/breseq/.deps/chisquare.Plo ./src/c/breseq/.deps/contingency_loci.Plo ./src/c/breseq/.deps/coverage_distribution.Plo ./src/c/breseq/.deps/coverage_output.Plo ./src/c/breseq/.deps/error_count.Plo ./src/c/breseq/.deps/fasta.Plo ./src/c/breseq/.deps/fastq.Plo ./src/c/breseq/.deps/gdtools_cmdline.Po ./src/c/breseq/.deps/genome_diff.Plo ./src/c/breseq/.deps/identify_mutations.Plo ./src/c/breseq/.deps/mutation_predictor.Plo ./src/c/breseq/.deps/output.Plo ./src/c/breseq/.deps/pileup.Plo ./src/c/breseq/.deps/pileup_base.Plo ./src/c/breseq/.deps/reference_sequence.Plo ./src/c/breseq/.deps/resolve_alignments.Plo ./src/c/breseq/.deps/rna_seq.Plo ./src/c/breseq/.deps/settings.Plo ./src/c/breseq/.deps/summary.Plo Looking for incorrect headers in 81 dependency files... Determining fink providers of 116 headers... 1 - 100 101 - 116 Found use of headers from 2 fink packages: gcc48-compiler libncurses5 Scanning binaries for incorrect dyld linking... /bin/rm -rf /sw/build.build/root-breseq-0.23-1 /bin/mkdir -p /sw/build.build/root-breseq-0.23-1/sw /bin/mkdir -p /sw/build.build/root-breseq-0.23-1/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-breseq-0.23-1 sudo -u fink-bld [ENV] sh -c /tmp/fink.QbuO5 make install DESTDIR=/sw/build.build/root-breseq-0.23-1 Making install in extern/samtools-0.1.18 Making install in bcftools ../../../aux_build/install-sh -c -d '/sw/build.build/root-breseq-0.23-1/sw/lib/breseq/bin' /bin/sh ../../../libtool --mode=install /usr/bin/install -c bcftools '/sw/build.build/root-breseq-0.23-1/sw/lib/breseq/bin' libtool: install: /usr/bin/install -c bcftools /sw/build.build/root-breseq-0.23-1/sw/lib/breseq/bin/bcftools make[3]: Nothing to be done for `install-data-am'. ../../aux_build/install-sh -c -d '/sw/build.build/root-breseq-0.23-1/sw/lib/breseq/bin' /bin/sh ../../libtool --mode=install /usr/bin/install -c samtools '/sw/build.build/root-breseq-0.23-1/sw/lib/breseq/bin' libtool: install: /usr/bin/install -c samtools /sw/build.build/root-breseq-0.23-1/sw/lib/breseq/bin/samtools ../../aux_build/install-sh -c -d '/sw/build.build/root-breseq-0.23-1/sw/lib/breseq/include' /usr/bin/install -c -m 644 bam.h '/sw/build.build/root-breseq-0.23-1/sw/lib/breseq/include' Making install in src/c/breseq ../../../aux_build/install-sh -c -d '/sw/build.build/root-breseq-0.23-1/sw/lib/breseq/bin' /bin/sh ../../../libtool --mode=install /usr/bin/install -c breseq gdtools '/sw/build.build/root-breseq-0.23-1/sw/lib/breseq/bin' libtool: install: /usr/bin/install -c breseq /sw/build.build/root-breseq-0.23-1/sw/lib/breseq/bin/breseq libtool: install: /usr/bin/install -c gdtools /sw/build.build/root-breseq-0.23-1/sw/lib/breseq/bin/gdtools mkdir -p /sw/build.build/root-breseq-0.23-1/sw/lib/breseq/share/breseq cp breseq.png /sw/build.build/root-breseq-0.23-1/sw/lib/breseq/share/breseq cp breseq_small.png /sw/build.build/root-breseq-0.23-1/sw/lib/breseq/share/breseq cp coverage_distribution.r /sw/build.build/root-breseq-0.23-1/sw/lib/breseq/share/breseq cp plot_coverage.r /sw/build.build/root-breseq-0.23-1/sw/lib/breseq/share/breseq cp plot_error_rate.r /sw/build.build/root-breseq-0.23-1/sw/lib/breseq/share/breseq cp plot_jc_scores.r /sw/build.build/root-breseq-0.23-1/sw/lib/breseq/share/breseq cp polymorphism_statistics.r /sw/build.build/root-breseq-0.23-1/sw/lib/breseq/share/breseq cp run_circos.sh /sw/build.build/root-breseq-0.23-1/sw/lib/breseq/share/breseq cp indels.conf /sw/build.build/root-breseq-0.23-1/sw/lib/breseq/share/breseq cp mutations.conf /sw/build.build/root-breseq-0.23-1/sw/lib/breseq/share/breseq cp karyotype.and.layout.conf /sw/build.build/root-breseq-0.23-1/sw/lib/breseq/share/breseq cp mobs.conf /sw/build.build/root-breseq-0.23-1/sw/lib/breseq/share/breseq cp ideogram.conf /sw/build.build/root-breseq-0.23-1/sw/lib/breseq/share/breseq cp combined_circos.conf /sw/build.build/root-breseq-0.23-1/sw/lib/breseq/share/breseq echo "export TESTBINPREFIX=/sw/build.build/breseq-0.23-1/breseq-0.23/src/c/breseq" > tests/test.config; echo "export BRESEQ_DATA_PATH=/sw/build.build/breseq-0.23-1/breseq-0.23/src/c/breseq" >> tests/test.config; echo "export BRESEQ_SAMTOOLS_PATH=/sw/build.build/breseq-0.23-1/breseq-0.23/extern/samtools-0.1.18" >> tests/test.config; make[2]: Nothing to be done for `install-exec-am'. make[2]: Nothing to be done for `install-data-am'. rm -r /sw/build.build/root-breseq-0.23-1/sw/lib/breseq/include install -m 0755 -d /sw/build.build/root-breseq-0.23-1/sw/bin ln -s /sw/lib/breseq/bin/breseq /sw/build.build/root-breseq-0.23-1/sw/bin/breseq sudo -u fink-bld [ENV] sh -c /tmp/fink.lc0yj /usr/bin/install -d -m 700 /sw/build.build/root-breseq-0.23-1/sw/share/doc/breseq /bin/cp -r AUTHORS /sw/build.build/root-breseq-0.23-1/sw/share/doc/breseq/ /bin/cp -r COPYING /sw/build.build/root-breseq-0.23-1/sw/share/doc/breseq/ /bin/cp -r NEWS /sw/build.build/root-breseq-0.23-1/sw/share/doc/breseq/ /bin/cp -r README /sw/build.build/root-breseq-0.23-1/sw/share/doc/breseq/ /bin/chmod -R go=u-w /sw/build.build/root-breseq-0.23-1/sw/share/doc/breseq /bin/rm -f /sw/build.build/root-breseq-0.23-1/sw/info/dir /sw/build.build/root-breseq-0.23-1/sw/info/dir.old /sw/build.build/root-breseq-0.23-1/sw/share/info/dir /sw/build.build/root-breseq-0.23-1/sw/share/info/dir.old Reverting ownership of install dir to root Writing control file... Writing conffiles list... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-breseq-0.23-1 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `breseq' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/breseq_0.23-1_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-breseq-0.23-1 (Reading database ... 12826 files and directories currently installed.) Removing fink-buildlock-breseq-0.23-1 ...