DC-Build-Header: qiime 1.5.0-1 / Sat Jun 23 16:17:54 +0000 2012 DC-Task: logfile:/tmp/qiime_1.5.0-1_unstable_clang.log version:1.5.0-1 chroot:unstable modes:binary-only:clang source:qiime architecture:any esttime:337 DC-Sbuild-call: su user -c 'sbuild -n --apt-update -d unstable -v --chroot-setup-commands=/tmp/switch-to-clang qiime_1.5.0-1' sbuild (Debian sbuild) 0.62.5 (13 Jul 2011) on ip-10-28-192-45.ec2.internal ╔══════════════════════════════════════════════════════════════════════════════╗ ║ qiime 1.5.0-1 (amd64) 23 Jun 2012 16:17 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: qiime Version: 1.5.0-1 Source Version: 1.5.0-1 Distribution: unstable Architecture: amd64 I: NOTICE: Log filtering will replace 'build/qiime-7HCqUr/qiime-1.5.0' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/qiime-7HCqUr' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-027338f0-fc07-4312-aa9f-f4357b9d7445' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Ign http://localhost unstable InRelease Get:1 http://localhost unstable Release.gpg [836 B] Get:2 http://localhost unstable Release [233 kB] Get:3 http://localhost unstable/main Sources/DiffIndex [7876 B] Get:4 http://localhost unstable/main amd64 Packages/DiffIndex [7876 B] Get:5 http://localhost unstable/main Translation-en/DiffIndex [7876 B] Get:6 http://localhost unstable/main 2012-06-23-0814.36.pdiff [8967 B] Get:7 http://localhost unstable/main 2012-06-23-0814.36.pdiff [8967 B] Get:8 http://localhost unstable/main amd64 2012-06-23-0814.36.pdiff [6101 B] Get:9 http://localhost unstable/main 2012-06-23-0814.36.pdiff [1297 B] Get:10 http://localhost unstable/main amd64 2012-06-23-0814.36.pdiff [6101 B] Get:11 http://localhost unstable/main 2012-06-23-0814.36.pdiff [1297 B] Fetched 274 kB in 4s (60.4 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'qiime' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/debian-med/trunk/packages/qiime/trunk/ Need to get 10.1 MB of source archives. Get:1 http://localhost/debian/ unstable/main qiime 1.5.0-1 (dsc) [1523 B] Get:2 http://localhost/debian/ unstable/main qiime 1.5.0-1 (tar) [10.1 MB] Get:3 http://localhost/debian/ unstable/main qiime 1.5.0-1 (diff) [11.8 kB] Fetched 10.1 MB in 0s (15.0 MB/s) Download complete and in download only mode Check arch ────────── ┌──────────────────────────────────────────────────────────────────────────────┐ │ Chroot Setup Commands │ └──────────────────────────────────────────────────────────────────────────────┘ /tmp/switch-to-clang ──────────────────── + echo 'Entering customization script...' Entering customization script... + apt-get update Ign http://localhost unstable InRelease Hit http://localhost unstable Release.gpg Hit http://localhost unstable Release Hit http://localhost unstable/main Sources/DiffIndex Hit http://localhost unstable/main amd64 Packages/DiffIndex Hit http://localhost unstable/main Translation-en/DiffIndex Reading package lists... + echo 'Install of clang' Install of clang + apt-get update Ign http://localhost unstable InRelease Hit http://localhost unstable Release.gpg Hit http://localhost unstable Release Hit http://localhost unstable/main Sources/DiffIndex Hit http://localhost unstable/main amd64 Packages/DiffIndex Hit http://localhost unstable/main Translation-en/DiffIndex Reading package lists... + apt-get install --yes --no-install-recommends clang -t unstable Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: libclang-common-dev libffi5 libllvm3.1 Recommended packages: llvm-3.1-dev python The following NEW packages will be installed: clang libclang-common-dev libffi5 libllvm3.1 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 13.1 MB of archives. After this operation, 35.6 MB of additional disk space will be used. Get:1 http://localhost/debian/ unstable/main libffi5 amd64 3.0.10-3 [24.8 kB] Get:2 http://localhost/debian/ unstable/main libllvm3.1 amd64 3.1-1 [7276 kB] Get:3 http://localhost/debian/ unstable/main libclang-common-dev amd64 3.1-6 [84.0 kB] Get:4 http://localhost/debian/ unstable/main clang amd64 3.1-6 [5755 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 13.1 MB in 0s (30.1 MB/s) Selecting previously unselected package libffi5:amd64. (Reading database ... 11730 files and directories currently installed.) Unpacking libffi5:amd64 (from .../libffi5_3.0.10-3_amd64.deb) ... Selecting previously unselected package libllvm3.1:amd64. Unpacking libllvm3.1:amd64 (from .../libllvm3.1_3.1-1_amd64.deb) ... Selecting previously unselected package libclang-common-dev. Unpacking libclang-common-dev (from .../libclang-common-dev_3.1-6_amd64.deb) ... Selecting previously unselected package clang. Unpacking clang (from .../archives/clang_3.1-6_amd64.deb) ... Setting up libffi5:amd64 (3.0.10-3) ... Setting up libllvm3.1:amd64 (3.1-1) ... Setting up libclang-common-dev (3.1-6) ... Setting up clang (3.1-6) ... + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSION=4.7 + cd /usr/bin + rm g++-4.7 gcc-4.7 cpp-4.7 + ln -s clang++ g++-4.7 + ln -s clang gcc-4.7 + ln -s clang cpp-4.7 + cd - /«BUILDDIR» + echo 'Block the installation of new gcc version' Block the installation of new gcc version + dpkg --set-selections + echo 'gcc-4.6 hold' + dpkg --set-selections + echo 'cpp-4.6 hold' + dpkg --set-selections + echo 'g++-4.6 hold' + dpkg --set-selections + echo 'gcc-4.7 hold' + dpkg --set-selections + echo 'cpp-4.7 hold' + dpkg --set-selections + echo 'g++-4.7 hold' + echo 'Check if gcc, g++ & cpp are actually clang' Check if gcc, g++ & cpp are actually clang + grep clang + gcc --version I: Finished running '/tmp/switch-to-clang'. Finished processing commands. ──────────────────────────────────────────────────────────────────────────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-yeXqix/apt_archive/sbuild-build-depends-core-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install core build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/708 B of archives. After this operation, 0 B of additional disk space will be used. Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 11810 files and directories currently installed.) Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), python-all-dev (>= 2.6), python-cogent (>= 1.5.1), python-numpy, python-matplotlib, ghc6, python-sphinx Filtered Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), python-all-dev (>= 2.6), python-cogent (>= 1.5.1), python-numpy, python-matplotlib, ghc6, python-sphinx dpkg-deb: building package `sbuild-build-depends-qiime-dummy' in `/«BUILDDIR»/resolver-JRTS_p/apt_archive/sbuild-build-depends-qiime-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install qiime build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils debhelper docutils-common file fontconfig fontconfig-config fonts-lyx gettext gettext-base ghc ghc6 gir1.2-glib-2.0 groff-base html2text intltool-debian libasprintf0c2 libatk1.0-0 libatk1.0-data libavahi-client3 libavahi-common-data libavahi-common3 libblas3 libblas3gf libbsd-dev libbsd0 libcairo2 libcroco3 libcups2 libdatrie1 libdb4.8 libdbus-1-3 libexpat1 libexpat1-dev libffi-dev libfontconfig1 libfreetype6 libgcrypt11 libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgettextpo0 libgfortran3 libgirepository-1.0-1 libglib2.0-0 libgmp-dev libgmpxx4ldbl libgnutls26 libgpg-error0 libgssapi-krb5-2 libgtk2.0-0 libgtk2.0-common libjasper1 libjbig0 libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblapack3gf libmagic1 libncursesw5 libp11-kit0 libpango1.0-0 libpcre3 libpipeline1 libpixman-1-0 libpng12-0 libpython2.6 libpython2.7 libsqlite3-0 libssl-dev libssl1.0.0 libtasn1-3 libthai-data libthai0 libtiff4 libunistring0 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxml2 libxrandr2 libxrender1 libxss1 man-db mime-support po-debconf python python-all python-all-dev python-cairo python-cogent python-dateutil python-dev python-docutils python-gi python-gobject python-gobject-2 python-jinja2 python-markupsafe python-matplotlib python-matplotlib-data python-minimal python-numpy python-pygments python-pyparsing python-roman python-sphinx python-support python-tz python2.6 python2.6-dev python2.6-minimal python2.7 python2.7-dev python2.7-minimal sgml-base shared-mime-info sphinx-common tcl8.5 tk8.5 ttf-dejavu-core x11-common xml-core zlib1g-dev Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc ghc-prof ghc-doc haskell-doc llvm-3.0 groff cups-common rng-tools libgmp10-doc libmpfr-dev krb5-doc krb5-user librsvg2-common gvfs libjasper-runtime ttf-baekmuk ttf-arphic-gbsn00lp ttf-arphic-bsmi00lp ttf-arphic-gkai00mp ttf-arphic-bkai00mp less www-browser libmail-box-perl python-doc python-tk texlive-latex-recommended texlive-latex-base texlive-lang-french fonts-linuxlibertine ttf-linux-libertine python-gi-cairo python-gobject-2-dbg python-jinja2-doc dvipng ipython python-configobj python-excelerator python-gtk2 python-matplotlib-doc python-qt4 python-scipy python-traits python-wxgtk2.8 texlive-extra-utils texlive-latex-extra python-numpy-doc python-numpy-dbg python-nose gfortran ttf-bitstream-vera jsmath libjs-mathjax texlive-fonts-recommended python2.6-doc binfmt-support python2.7-doc sgml-base-doc tcl-tclreadline Recommended packages: curl wget lynx-cur autopoint dbus libglib2.0-data hicolor-icon-theme libgtk2.0-bin javascript-common krb5-locales libgpm2 libssl-doc libmail-sendmail-perl python-imaging libpaper-utils python-lxml docutils-doc python-pkg-resources python-glade2 python-chardet sphinx-doc xterm x-terminal-emulator The following NEW packages will be installed: bsdmainutils debhelper docutils-common file fontconfig fontconfig-config fonts-lyx gettext gettext-base ghc ghc6 gir1.2-glib-2.0 groff-base html2text intltool-debian libasprintf0c2 libatk1.0-0 libatk1.0-data libavahi-client3 libavahi-common-data libavahi-common3 libblas3 libblas3gf libbsd-dev libbsd0 libcairo2 libcroco3 libcups2 libdatrie1 libdb4.8 libdbus-1-3 libexpat1 libexpat1-dev libffi-dev libfontconfig1 libfreetype6 libgcrypt11 libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgettextpo0 libgfortran3 libgirepository-1.0-1 libglib2.0-0 libgmp-dev libgmpxx4ldbl libgnutls26 libgpg-error0 libgssapi-krb5-2 libgtk2.0-0 libgtk2.0-common libjasper1 libjbig0 libjpeg8 libjs-jquery libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblapack3gf libmagic1 libncursesw5 libp11-kit0 libpango1.0-0 libpcre3 libpipeline1 libpixman-1-0 libpng12-0 libpython2.6 libpython2.7 libsqlite3-0 libssl-dev libssl1.0.0 libtasn1-3 libthai-data libthai0 libtiff4 libunistring0 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxml2 libxrandr2 libxrender1 libxss1 man-db mime-support po-debconf python python-all python-all-dev python-cairo python-cogent python-dateutil python-dev python-docutils python-gi python-gobject python-gobject-2 python-jinja2 python-markupsafe python-matplotlib python-matplotlib-data python-minimal python-numpy python-pygments python-pyparsing python-roman python-sphinx python-support python-tz python2.6 python2.6-dev python2.6-minimal python2.7 python2.7-dev python2.7-minimal sbuild-build-depends-qiime-dummy sgml-base shared-mime-info sphinx-common tcl8.5 tk8.5 ttf-dejavu-core x11-common xml-core zlib1g-dev 0 upgraded, 141 newly installed, 0 to remove and 0 not upgraded. Need to get 143 MB/143 MB of archives. After this operation, 542 MB of additional disk space will be used. Get:1 http://localhost/debian/ unstable/main libncursesw5 amd64 5.9-9 [141 kB] Get:2 http://localhost/debian/ unstable/main libpipeline1 amd64 1.2.1-1 [39.2 kB] Get:3 http://localhost/debian/ unstable/main libssl1.0.0 amd64 1.0.1c-3 [1211 kB] Get:4 http://localhost/debian/ unstable/main libasprintf0c2 amd64 0.18.1.1-9 [26.8 kB] Get:5 http://localhost/debian/ unstable/main libgpg-error0 amd64 1.10-3 [66.8 kB] Get:6 http://localhost/debian/ unstable/main libgcrypt11 amd64 1.5.0-3 [298 kB] Get:7 http://localhost/debian/ unstable/main libp11-kit0 amd64 0.12-3 [52.8 kB] Get:8 http://localhost/debian/ unstable/main libtasn1-3 amd64 2.13-2 [67.7 kB] Get:9 http://localhost/debian/ unstable/main libgnutls26 amd64 2.12.20-1 [616 kB] Get:10 http://localhost/debian/ unstable/main libkeyutils1 amd64 1.5.5-2 [9300 B] Get:11 http://localhost/debian/ unstable/main libkrb5support0 amd64 1.10.1+dfsg-1 [49.0 kB] Get:12 http://localhost/debian/ unstable/main libk5crypto3 amd64 1.10.1+dfsg-1 [112 kB] Get:13 http://localhost/debian/ unstable/main libkrb5-3 amd64 1.10.1+dfsg-1 [393 kB] Get:14 http://localhost/debian/ unstable/main libgssapi-krb5-2 amd64 1.10.1+dfsg-1 [147 kB] Get:15 http://localhost/debian/ unstable/main libmagic1 amd64 5.11-1 [250 kB] Get:16 http://localhost/debian/ unstable/main libpcre3 amd64 1:8.30-5 [242 kB] Get:17 http://localhost/debian/ unstable/main libsqlite3-0 amd64 3.7.13-1 [455 kB] Get:18 http://localhost/debian/ unstable/main libxml2 amd64 2.8.0+dfsg1-4 [903 kB] Get:19 http://localhost/debian/ unstable/main libglib2.0-0 amd64 2.32.3-1 [2081 kB] Get:20 http://localhost/debian/ unstable/main libatk1.0-data all 2.4.0-2 [240 kB] Get:21 http://localhost/debian/ unstable/main libatk1.0-0 amd64 2.4.0-2 [95.1 kB] Get:22 http://localhost/debian/ unstable/main libavahi-common-data amd64 0.6.31-1 [134 kB] Get:23 http://localhost/debian/ unstable/main libavahi-common3 amd64 0.6.31-1 [54.3 kB] Get:24 http://localhost/debian/ unstable/main libdbus-1-3 amd64 1.6.0-1 [171 kB] Get:25 http://localhost/debian/ unstable/main libavahi-client3 amd64 0.6.31-1 [59.1 kB] Get:26 http://localhost/debian/ unstable/main libbsd0 amd64 0.4.0-1 [54.7 kB] Get:27 http://localhost/debian/ unstable/main libexpat1 amd64 2.1.0-1 [141 kB] Get:28 http://localhost/debian/ unstable/main libfreetype6 amd64 2.4.9-1 [450 kB] Get:29 http://localhost/debian/ unstable/main ttf-dejavu-core all 2.33-2 [1552 kB] Get:30 http://localhost/debian/ unstable/main fontconfig-config all 2.9.0-6 [232 kB] Get:31 http://localhost/debian/ unstable/main libfontconfig1 amd64 2.9.0-6 [299 kB] Get:32 http://localhost/debian/ unstable/main libpixman-1-0 amd64 0.26.0-2 [427 kB] Get:33 http://localhost/debian/ unstable/main libpng12-0 amd64 1.2.49-1 [190 kB] Get:34 http://localhost/debian/ unstable/main libxau6 amd64 1:1.0.7-1 [18.8 kB] Get:35 http://localhost/debian/ unstable/main libxdmcp6 amd64 1:1.1.1-1 [26.3 kB] Get:36 http://localhost/debian/ unstable/main libxcb1 amd64 1.8.1-1 [50.0 kB] Get:37 http://localhost/debian/ unstable/main libx11-data all 2:1.5.0-1 [189 kB] Get:38 http://localhost/debian/ unstable/main libx11-6 amd64 2:1.5.0-1 [901 kB] Get:39 http://localhost/debian/ unstable/main libxcb-render0 amd64 1.8.1-1 [18.4 kB] Get:40 http://localhost/debian/ unstable/main libxcb-shm0 amd64 1.8.1-1 [10.1 kB] Get:41 http://localhost/debian/ unstable/main libxrender1 amd64 1:0.9.7-1 [32.2 kB] Get:42 http://localhost/debian/ unstable/main libcairo2 amd64 1.12.2-2 [912 kB] Get:43 http://localhost/debian/ unstable/main libcroco3 amd64 0.6.5-1 [151 kB] Get:44 http://localhost/debian/ unstable/main libcups2 amd64 1.5.3-2 [255 kB] Get:45 http://localhost/debian/ unstable/main libdatrie1 amd64 0.2.5-3 [28.6 kB] Get:46 http://localhost/debian/ unstable/main libjpeg8 amd64 8d-1 [134 kB] Get:47 http://localhost/debian/ unstable/main libjasper1 amd64 1.900.1-13 [159 kB] Get:48 http://localhost/debian/ unstable/main libjbig0 amd64 2.0-2 [32.2 kB] Get:49 http://localhost/debian/ unstable/main libtiff4 amd64 3.9.6-5 [201 kB] Get:50 http://localhost/debian/ unstable/main libgdk-pixbuf2.0-common all 2.26.1-1 [497 kB] Get:51 http://localhost/debian/ unstable/main libgdk-pixbuf2.0-0 amd64 2.26.1-1 [207 kB] Get:52 http://localhost/debian/ unstable/main libunistring0 amd64 0.9.3-5 [434 kB] Get:53 http://localhost/debian/ unstable/main libgettextpo0 amd64 0.18.1.1-9 [145 kB] Get:54 http://localhost/debian/ unstable/main libgfortran3 amd64 4.7.1-1 [352 kB] Get:55 http://localhost/debian/ unstable/main libgmpxx4ldbl amd64 2:5.0.5+dfsg-2 [21.6 kB] Get:56 http://localhost/debian/ unstable/main libgtk2.0-common all 2.24.10-1 [6879 kB] Get:57 http://localhost/debian/ unstable/main libthai-data all 0.1.18-1 [205 kB] Get:58 http://localhost/debian/ unstable/main libthai0 amd64 0.1.18-1 [45.0 kB] Get:59 http://localhost/debian/ unstable/main libxft2 amd64 2.3.1-1 [61.0 kB] Get:60 http://localhost/debian/ unstable/main fontconfig amd64 2.9.0-6 [349 kB] Get:61 http://localhost/debian/ unstable/main libpango1.0-0 amd64 1.30.0-1 [461 kB] Get:62 http://localhost/debian/ unstable/main libxcomposite1 amd64 1:0.4.3-2 [16.6 kB] Get:63 http://localhost/debian/ unstable/main libxfixes3 amd64 1:5.0-4 [21.5 kB] Get:64 http://localhost/debian/ unstable/main libxcursor1 amd64 1:1.1.13-1 [26.9 kB] Get:65 http://localhost/debian/ unstable/main libxdamage1 amd64 1:1.1.3-2 [14.3 kB] Get:66 http://localhost/debian/ unstable/main libxext6 amd64 2:1.3.1-2 [55.3 kB] Get:67 http://localhost/debian/ unstable/main libxi6 amd64 2:1.6.1-1 [75.0 kB] Get:68 http://localhost/debian/ unstable/main libxinerama1 amd64 2:1.1.2-1 [16.8 kB] Get:69 http://localhost/debian/ unstable/main libxrandr2 amd64 2:1.3.2-2 [33.5 kB] Get:70 http://localhost/debian/ unstable/main shared-mime-info amd64 1.0-1 [1066 kB] Get:71 http://localhost/debian/ unstable/main libgtk2.0-0 amd64 2.24.10-1 [2730 kB] Get:72 http://localhost/debian/ unstable/main x11-common all 1:7.6+13 [278 kB] Get:73 http://localhost/debian/ unstable/main libxss1 amd64 1:1.2.2-1 [17.5 kB] Get:74 http://localhost/debian/ unstable/main libdb4.8 amd64 4.8.30-11 [694 kB] Get:75 http://localhost/debian/ unstable/main bsdmainutils amd64 9.0.3 [209 kB] Get:76 http://localhost/debian/ unstable/main groff-base amd64 1.21-8 [1152 kB] Get:77 http://localhost/debian/ unstable/main man-db amd64 2.6.2-1 [1061 kB] Get:78 http://localhost/debian/ unstable/main file amd64 5.11-1 [53.2 kB] Get:79 http://localhost/debian/ unstable/main gettext-base amd64 0.18.1.1-9 [154 kB] Get:80 http://localhost/debian/ unstable/main mime-support all 3.52-1 [35.5 kB] Get:81 http://localhost/debian/ unstable/main python2.7-minimal amd64 2.7.3-1 [1770 kB] Get:82 http://localhost/debian/ unstable/main python2.7 amd64 2.7.3-1 [2726 kB] Get:83 http://localhost/debian/ unstable/main python-minimal all 2.7.3~rc2-1 [40.4 kB] Get:84 http://localhost/debian/ unstable/main python all 2.7.3~rc2-1 [179 kB] Get:85 http://localhost/debian/ unstable/main python-support all 1.0.14 [33.5 kB] Get:86 http://localhost/debian/ unstable/main python2.6-minimal amd64 2.6.7-4 [1524 kB] Get:87 http://localhost/debian/ unstable/main python2.6 amd64 2.6.7-4 [2483 kB] Get:88 http://localhost/debian/ unstable/main html2text amd64 1.3.2a-15 [103 kB] Get:89 http://localhost/debian/ unstable/main gettext amd64 0.18.1.1-9 [1975 kB] Get:90 http://localhost/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB] Get:91 http://localhost/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB] Get:92 http://localhost/debian/ unstable/main debhelper all 9.20120608 [700 kB] Get:93 http://localhost/debian/ unstable/main sgml-base all 1.26+nmu3 [13.5 kB] Get:94 http://localhost/debian/ unstable/main xml-core all 0.13+nmu1 [23.8 kB] Get:95 http://localhost/debian/ unstable/main docutils-common all 0.8.1-7 [196 kB] Get:96 http://localhost/debian/ unstable/main fonts-lyx all 2.0.3-3 [167 kB] Get:97 http://localhost/debian/ unstable/main libgmp-dev amd64 2:5.0.5+dfsg-2 [610 kB] Get:98 http://localhost/debian/ unstable/main libffi-dev amd64 3.0.10-3 [116 kB] Get:99 http://localhost/debian/ unstable/main libbsd-dev amd64 0.4.0-1 [135 kB] Get:100 http://localhost/debian/ unstable/main ghc amd64 7.4.1-4 [45.8 MB] Get:101 http://localhost/debian/ unstable/main ghc6 all 7.4.1-4 [26.9 kB] Get:102 http://localhost/debian/ unstable/main libgirepository-1.0-1 amd64 1.32.1-1 [107 kB] Get:103 http://localhost/debian/ unstable/main gir1.2-glib-2.0 amd64 1.32.1-1 [171 kB] Get:104 http://localhost/debian/ unstable/main libblas3 amd64 1.2.20110419-3 [293 kB] Get:105 http://localhost/debian/ unstable/main libblas3gf amd64 1.2.20110419-3 [7804 B] Get:106 http://localhost/debian/ unstable/main libexpat1-dev amd64 2.1.0-1 [229 kB] Get:107 http://localhost/debian/ unstable/main libjs-jquery all 1.7.2+debian-2 [113 kB] Get:108 http://localhost/debian/ unstable/main libjs-underscore all 1.3.3-1 [42.6 kB] Get:109 http://localhost/debian/ unstable/main libjs-sphinxdoc all 1.1.3+dfsg-4 [43.8 kB] Get:110 http://localhost/debian/ unstable/main liblapack3 amd64 3.4.1-3 [5035 kB] Get:111 http://localhost/debian/ unstable/main liblapack3gf amd64 3.4.1-3 [10.5 kB] Get:112 http://localhost/debian/ unstable/main libpython2.6 amd64 2.6.7-4 [1087 kB] Get:113 http://localhost/debian/ unstable/main libpython2.7 amd64 2.7.3-1 [1212 kB] Get:114 http://localhost/debian/ unstable/main zlib1g-dev amd64 1:1.2.7.dfsg-13 [215 kB] Get:115 http://localhost/debian/ unstable/main libssl-dev amd64 1.0.1c-3 [1696 kB] Get:116 http://localhost/debian/ unstable/main python-all all 2.7.3~rc2-1 [880 B] Get:117 http://localhost/debian/ unstable/main python2.7-dev amd64 2.7.3-1 [22.3 MB] Get:118 http://localhost/debian/ unstable/main python-dev all 2.7.3~rc2-1 [912 B] Get:119 http://localhost/debian/ unstable/main python2.6-dev amd64 2.6.7-4 [4832 kB] Get:120 http://localhost/debian/ unstable/main python-all-dev all 2.7.3~rc2-1 [894 B] Get:121 http://localhost/debian/ unstable/main python-cairo amd64 1.8.8-1+b2 [84.2 kB] Get:122 http://localhost/debian/ unstable/main python-dateutil all 1.5-1 [53.8 kB] Get:123 http://localhost/debian/ unstable/main python-roman all 0.8.1-7 [51.9 kB] Get:124 http://localhost/debian/ unstable/main python-docutils all 0.8.1-7 [392 kB] Get:125 http://localhost/debian/ unstable/main python-gi amd64 3.2.2-1 [518 kB] Get:126 http://localhost/debian/ unstable/main python-gobject-2 amd64 2.28.6-10 [555 kB] Get:127 http://localhost/debian/ unstable/main python-gobject all 3.2.2-1 [162 kB] Get:128 http://localhost/debian/ unstable/main python-markupsafe amd64 0.15-1 [14.6 kB] Get:129 http://localhost/debian/ unstable/main python-jinja2 amd64 2.6-1 [168 kB] Get:130 http://localhost/debian/ unstable/main python-matplotlib-data all 1.1.1~rc2-1 [2057 kB] Get:131 http://localhost/debian/ unstable/main python-pyparsing all 1.5.6+dfsg1-1 [64.8 kB] Get:132 http://localhost/debian/ unstable/main python-tz all 2012c-1 [39.9 kB] Get:133 http://localhost/debian/ unstable/main python-numpy amd64 1:1.6.2-1 [2631 kB] Get:134 http://localhost/debian/ unstable/main tcl8.5 amd64 8.5.11-2 [1627 kB] Get:135 http://localhost/debian/ unstable/main tk8.5 amd64 8.5.11-2 [1189 kB] Get:136 http://localhost/debian/ unstable/main python-matplotlib amd64 1.1.1~rc2-1 [2695 kB] Get:137 http://localhost/debian/ unstable/main python-pygments all 1.5+dfsg-1 [451 kB] Get:138 http://localhost/debian/ unstable/main sphinx-common all 1.1.3+dfsg-4 [412 kB] Get:139 http://localhost/debian/ unstable/main python-sphinx all 1.1.3+dfsg-4 [311 kB] Get:140 http://localhost/debian/ unstable/main python-cogent amd64 1.5.1-2 [1898 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 143 MB in 6s (21.5 MB/s) Selecting previously unselected package libncursesw5:amd64. (Reading database ... 11810 files and directories currently installed.) Unpacking libncursesw5:amd64 (from .../libncursesw5_5.9-9_amd64.deb) ... Selecting previously unselected package libpipeline1:amd64. Unpacking libpipeline1:amd64 (from .../libpipeline1_1.2.1-1_amd64.deb) ... Selecting previously unselected package libssl1.0.0:amd64. Unpacking libssl1.0.0:amd64 (from .../libssl1.0.0_1.0.1c-3_amd64.deb) ... Selecting previously unselected package libasprintf0c2:amd64. Unpacking libasprintf0c2:amd64 (from .../libasprintf0c2_0.18.1.1-9_amd64.deb) ... Selecting previously unselected package libgpg-error0:amd64. Unpacking libgpg-error0:amd64 (from .../libgpg-error0_1.10-3_amd64.deb) ... Selecting previously unselected package libgcrypt11:amd64. Unpacking libgcrypt11:amd64 (from .../libgcrypt11_1.5.0-3_amd64.deb) ... Selecting previously unselected package libp11-kit0:amd64. Unpacking libp11-kit0:amd64 (from .../libp11-kit0_0.12-3_amd64.deb) ... 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Setting up libssl1.0.0:amd64 (1.0.1c-3) ... Setting up libasprintf0c2:amd64 (0.18.1.1-9) ... Setting up libgpg-error0:amd64 (1.10-3) ... Setting up libgcrypt11:amd64 (1.5.0-3) ... Setting up libp11-kit0:amd64 (0.12-3) ... Setting up libtasn1-3:amd64 (2.13-2) ... Setting up libgnutls26:amd64 (2.12.20-1) ... Setting up libkeyutils1:amd64 (1.5.5-2) ... Setting up libkrb5support0:amd64 (1.10.1+dfsg-1) ... Setting up libk5crypto3:amd64 (1.10.1+dfsg-1) ... Setting up libkrb5-3:amd64 (1.10.1+dfsg-1) ... Setting up libgssapi-krb5-2:amd64 (1.10.1+dfsg-1) ... Setting up libmagic1:amd64 (5.11-1) ... Setting up libpcre3:amd64 (1:8.30-5) ... Setting up libsqlite3-0:amd64 (3.7.13-1) ... Setting up libxml2:amd64 (2.8.0+dfsg1-4) ... Setting up libglib2.0-0:amd64 (2.32.3-1) ... No schema files found: doing nothing. Setting up libatk1.0-data (2.4.0-2) ... Setting up libatk1.0-0:amd64 (2.4.0-2) ... Setting up libavahi-common-data:amd64 (0.6.31-1) ... Setting up libavahi-common3:amd64 (0.6.31-1) ... Setting up libdbus-1-3:amd64 (1.6.0-1) ... Setting up libavahi-client3:amd64 (0.6.31-1) ... Setting up libbsd0:amd64 (0.4.0-1) ... Setting up libexpat1:amd64 (2.1.0-1) ... Setting up libfreetype6:amd64 (2.4.9-1) ... Setting up ttf-dejavu-core (2.33-2) ... Setting up fontconfig-config (2.9.0-6) ... Setting up libfontconfig1:amd64 (2.9.0-6) ... Setting up libpixman-1-0:amd64 (0.26.0-2) ... Setting up libpng12-0:amd64 (1.2.49-1) ... Setting up libxau6:amd64 (1:1.0.7-1) ... Setting up libxdmcp6:amd64 (1:1.1.1-1) ... Setting up libxcb1:amd64 (1.8.1-1) ... Setting up libx11-data (2:1.5.0-1) ... Setting up libx11-6:amd64 (2:1.5.0-1) ... Setting up libxcb-render0:amd64 (1.8.1-1) ... Setting up libxcb-shm0:amd64 (1.8.1-1) ... Setting up libxrender1:amd64 (1:0.9.7-1) ... Setting up libcairo2:amd64 (1.12.2-2) ... Setting up libcroco3:amd64 (0.6.5-1) ... Setting up libcups2:amd64 (1.5.3-2) ... Setting up libdatrie1:amd64 (0.2.5-3) ... Setting up libjpeg8:amd64 (8d-1) ... Setting up libjasper1:amd64 (1.900.1-13) ... Setting up libjbig0:amd64 (2.0-2) ... Setting up libtiff4:amd64 (3.9.6-5) ... Setting up libgdk-pixbuf2.0-common (2.26.1-1) ... Setting up libgdk-pixbuf2.0-0:amd64 (2.26.1-1) ... Setting up libunistring0:amd64 (0.9.3-5) ... Setting up libgettextpo0:amd64 (0.18.1.1-9) ... Setting up libgfortran3:amd64 (4.7.1-1) ... Setting up libgmpxx4ldbl:amd64 (2:5.0.5+dfsg-2) ... Setting up libgtk2.0-common (2.24.10-1) ... Setting up libthai-data (0.1.18-1) ... Setting up libthai0:amd64 (0.1.18-1) ... Setting up libxft2:amd64 (2.3.1-1) ... Setting up fontconfig (2.9.0-6) ... Cleaning up old fontconfig caches... done. Regenerating fonts cache... done. Setting up libpango1.0-0:amd64 (1.30.0-1) ... Setting up libxcomposite1:amd64 (1:0.4.3-2) ... Setting up libxfixes3:amd64 (1:5.0-4) ... Setting up libxcursor1:amd64 (1:1.1.13-1) ... Setting up libxdamage1:amd64 (1:1.1.3-2) ... Setting up libxext6:amd64 (2:1.3.1-2) ... Setting up libxi6:amd64 (2:1.6.1-1) ... Setting up libxinerama1:amd64 (2:1.1.2-1) ... Setting up libxrandr2:amd64 (2:1.3.2-2) ... Setting up shared-mime-info (1.0-1) ... Setting up libgtk2.0-0:amd64 (2.24.10-1) ... Setting up x11-common (1:7.6+13) ... All runlevel operations denied by policy invoke-rc.d: policy-rc.d denied execution of start. Setting up libxss1:amd64 (1:1.2.2-1) ... Setting up libdb4.8:amd64 (4.8.30-11) ... Setting up bsdmainutils (9.0.3) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode. update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode. Setting up groff-base (1.21-8) ... Setting up man-db (2.6.2-1) ... Building database of manual pages ... Setting up file (5.11-1) ... Setting up gettext-base (0.18.1.1-9) ... Setting up mime-support (3.52-1) ... update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode. Setting up python2.7-minimal (2.7.3-1) ... Setting up python2.7 (2.7.3-1) ... Setting up python-minimal (2.7.3~rc2-1) ... Setting up python (2.7.3~rc2-1) ... Setting up python-support (1.0.14) ... Setting up python2.6-minimal (2.6.7-4) ... Setting up python2.6 (2.6.7-4) ... Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-9) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20120608) ... Setting up sgml-base (1.26+nmu3) ... Updating the super catalog... Setting up xml-core (0.13+nmu1) ... Setting up fonts-lyx (2.0.3-3) ... Setting up libgmp-dev:amd64 (2:5.0.5+dfsg-2) ... Setting up libffi-dev:amd64 (3.0.10-3) ... Setting up libbsd-dev (0.4.0-1) ... Setting up ghc (7.4.1-4) ... update-alternatives: using /usr/bin/runghc to provide /usr/bin/runhaskell (runhaskell) in auto mode. update-alternatives: using /usr/bin/ghc to provide /usr/bin/haskell-compiler (haskell-compiler) in auto mode. Setting up ghc6 (7.4.1-4) ... Setting up libgirepository-1.0-1 (1.32.1-1) ... Setting up gir1.2-glib-2.0 (1.32.1-1) ... Setting up libblas3 (1.2.20110419-3) ... update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode. Setting up libblas3gf (1.2.20110419-3) ... Setting up libexpat1-dev (2.1.0-1) ... Setting up libjs-jquery (1.7.2+debian-2) ... Setting up libjs-underscore (1.3.3-1) ... Setting up libjs-sphinxdoc (1.1.3+dfsg-4) ... Setting up liblapack3 (3.4.1-3) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode. Setting up liblapack3gf (3.4.1-3) ... Setting up libpython2.6 (2.6.7-4) ... Setting up libpython2.7 (2.7.3-1) ... Setting up zlib1g-dev:amd64 (1:1.2.7.dfsg-13) ... Setting up libssl-dev (1.0.1c-3) ... Setting up python-all (2.7.3~rc2-1) ... Setting up python2.7-dev (2.7.3-1) ... Setting up python-dev (2.7.3~rc2-1) ... Setting up python2.6-dev (2.6.7-4) ... Setting up python-all-dev (2.7.3~rc2-1) ... Setting up python-cairo (1.8.8-1+b2) ... Setting up python-dateutil (1.5-1) ... Setting up python-roman (0.8.1-7) ... Setting up python-gi (3.2.2-1) ... Setting up python-gobject-2 (2.28.6-10) ... Setting up python-gobject (3.2.2-1) ... Setting up python-markupsafe (0.15-1) ... Setting up python-jinja2 (2.6-1) ... Setting up python-matplotlib-data (1.1.1~rc2-1) ... Setting up python-pyparsing (1.5.6+dfsg1-1) ... Setting up python-tz (2012c-1) ... Setting up python-numpy (1:1.6.2-1) ... Setting up tcl8.5 (8.5.11-2) ... update-alternatives: using /usr/bin/tclsh8.5 to provide /usr/bin/tclsh (tclsh) in auto mode. Setting up tk8.5 (8.5.11-2) ... update-alternatives: using /usr/bin/wish8.5 to provide /usr/bin/wish (wish) in auto mode. Setting up python-matplotlib (1.1.1~rc2-1) ... Setting up python-pygments (1.5+dfsg-1) ... Setting up sphinx-common (1.1.3+dfsg-4) ... Setting up python-cogent (1.5.1-2) ... Processing triggers for sgml-base ... Updating the super catalog... Setting up docutils-common (0.8.1-7) ... Processing triggers for sgml-base ... Updating the super catalog... Setting up python-docutils (0.8.1-7) ... update-alternatives: using /usr/share/docutils/scripts/python2/rst-buildhtml to provide /usr/bin/rst-buildhtml (rst-buildhtml) in auto mode. update-alternatives: using /usr/share/docutils/scripts/python2/rst2html to provide /usr/bin/rst2html (rst2html) in auto mode. update-alternatives: using /usr/share/docutils/scripts/python2/rst2latex to provide /usr/bin/rst2latex (rst2latex) in auto mode. update-alternatives: using /usr/share/docutils/scripts/python2/rst2man to provide /usr/bin/rst2man (rst2man) in auto mode. update-alternatives: using /usr/share/docutils/scripts/python2/rst2odt to provide /usr/bin/rst2odt (rst2odt) in auto mode. update-alternatives: using /usr/share/docutils/scripts/python2/rst2odt_prepstyles to provide /usr/bin/rst2odt_prepstyles (rst2odt_prepstyles) in auto mode. update-alternatives: using /usr/share/docutils/scripts/python2/rst2pseudoxml to provide /usr/bin/rst2pseudoxml (rst2pseudoxml) in auto mode. update-alternatives: using /usr/share/docutils/scripts/python2/rst2s5 to provide /usr/bin/rst2s5 (rst2s5) in auto mode. update-alternatives: using /usr/share/docutils/scripts/python2/rst2xetex to provide /usr/bin/rst2xetex (rst2xetex) in auto mode. update-alternatives: using /usr/share/docutils/scripts/python2/rst2xml to provide /usr/bin/rst2xml (rst2xml) in auto mode. update-alternatives: using /usr/share/docutils/scripts/python2/rstpep2html to provide /usr/bin/rstpep2html (rstpep2html) in auto mode. Setting up python-sphinx (1.1.3+dfsg-4) ... Setting up sbuild-build-depends-qiime-dummy (0.invalid.0) ... Processing triggers for python-support ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 2.6.32-5-xen-amd64 amd64 (x86_64) Toolchain package versions: binutils_2.22-6.1 dpkg-dev_1.16.4.3 g++-4.6_4.6.3-7 g++-4.7_4.7.1-1 gcc-4.6_4.6.3-7 gcc-4.7_4.7.1-1 libc6-dev_2.13-33 libstdc++6_4.7.1-1 libstdc++6-4.6-dev_4.6.3-7 libstdc++6-4.7-dev_4.7.1-1 linux-libc-dev_3.2.20-1 Package versions: apt_0.9.7 base-files_6.11 base-passwd_3.5.25 bash_4.2-2 binutils_2.22-6.1 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5 build-essential_11.5 bzip2_1.0.6-3 clang_3.1-6 coreutils_8.13-3.2 cpp_4:4.7.0-6 cpp-4.6_4.6.3-7 cpp-4.7_4.7.1-1 dash_0.5.7-3 debconf_1.5.44 debconf-i18n_1.5.44 debfoster_2.7-1.1 debhelper_9.20120608 debian-archive-keyring_2012.4 debianutils_4.3.1 diffutils_1:3.2-6 docutils-common_0.8.1-7 dpkg_1.16.4.3 dpkg-dev_1.16.4.3 e2fslibs_1.42.4-3 e2fsprogs_1.42.4-3 fakeroot_1.18.4-2 file_5.11-1 findutils_4.4.2-4 fontconfig_2.9.0-6 fontconfig-config_2.9.0-6 fonts-lyx_2.0.3-3 g++_4:4.7.0-6 g++-4.6_4.6.3-7 g++-4.7_4.7.1-1 gcc_4:4.7.0-6 gcc-4.4-base_4.4.7-1 gcc-4.5-base_4.5.3-12 gcc-4.6_4.6.3-7 gcc-4.6-base_4.6.3-7 gcc-4.7_4.7.1-1 gcc-4.7-base_4.7.1-1 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 ghc_7.4.1-4 ghc6_7.4.1-4 gir1.2-glib-2.0_1.32.1-1 gnupg_1.4.12-4 gpgv_1.4.12-4 grep_2.12-2 groff-base_1.21-8 gzip_1.5-1.1 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-27 insserv_1.14.0-3 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7 libasprintf0c2_0.18.1.1-9 libatk1.0-0_2.4.0-2 libatk1.0-data_2.4.0-2 libattr1_1:2.4.46-8 libavahi-client3_0.6.31-1 libavahi-common-data_0.6.31-1 libavahi-common3_0.6.31-1 libblas3_1.2.20110419-3 libblas3gf_1.2.20110419-3 libblkid1_2.20.1-5 libbsd-dev_0.4.0-1 libbsd0_0.4.0-1 libbz2-1.0_1.0.6-3 libc-bin_2.13-33 libc-dev-bin_2.13-33 libc6_2.13-33 libc6-dev_2.13-33 libcairo2_1.12.2-2 libclang-common-dev_3.1-6 libclass-isa-perl_0.36-3 libcomerr2_1.42.4-3 libcroco3_0.6.5-1 libcups2_1.5.3-2 libdatrie1_0.2.5-3 libdb4.8_4.8.30-11 libdb5.1_5.1.29-4 libdbus-1-3_1.6.0-1 libdpkg-perl_1.16.4.3 libexpat1_2.1.0-1 libexpat1-dev_2.1.0-1 libffi-dev_3.0.10-3 libffi5_3.0.10-3 libfile-fcntllock-perl_0.14-2 libfontconfig1_2.9.0-6 libfreetype6_2.4.9-1 libgc1c2_1:7.1-8 libgcc1_1:4.7.1-1 libgcrypt11_1.5.0-3 libgdbm3_1.8.3-11 libgdk-pixbuf2.0-0_2.26.1-1 libgdk-pixbuf2.0-common_2.26.1-1 libgettextpo0_0.18.1.1-9 libgfortran3_4.7.1-1 libgirepository-1.0-1_1.32.1-1 libglib2.0-0_2.32.3-1 libgmp-dev_2:5.0.5+dfsg-2 libgmp10_2:5.0.5+dfsg-2 libgmpxx4ldbl_2:5.0.5+dfsg-2 libgnutls26_2.12.20-1 libgomp1_4.7.1-1 libgpg-error0_1.10-3 libgssapi-krb5-2_1.10.1+dfsg-1 libgtk2.0-0_2.24.10-1 libgtk2.0-common_2.24.10-1 libitm1_4.7.1-1 libjasper1_1.900.1-13 libjbig0_2.0-2 libjpeg8_8d-1 libjs-jquery_1.7.2+debian-2 libjs-sphinxdoc_1.1.3+dfsg-4 libjs-underscore_1.3.3-1 libk5crypto3_1.10.1+dfsg-1 libkeyutils1_1.5.5-2 libkrb5-3_1.10.1+dfsg-1 libkrb5support0_1.10.1+dfsg-1 liblapack3_3.4.1-3 liblapack3gf_3.4.1-3 libllvm3.1_3.1-1 liblocale-gettext-perl_1.05-7+b1 liblzma5_5.1.1alpha+20120614-1 libmagic1_5.11-1 libmount1_2.20.1-5 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-9 libncursesw5_5.9-9 libp11-kit0_0.12-3 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpango1.0-0_1.30.0-1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libpixman-1-0_0.26.0-2 libpng12-0_1.2.49-1 libpython2.6_2.6.7-4 libpython2.7_2.7.3-1 libquadmath0_4.7.1-1 libreadline6_6.2-8 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-13 libsqlite3-0_3.7.13-1 libss2_1.42.4-3 libssl-dev_1.0.1c-3 libssl1.0.0_1.0.1c-3 libstdc++6_4.7.1-1 libstdc++6-4.6-dev_4.6.3-7 libstdc++6-4.7-dev_4.7.1-1 libswitch-perl_2.16-2 libtasn1-3_2.13-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libthai-data_0.1.18-1 libthai0_0.1.18-1 libtiff4_3.9.6-5 libtimedate-perl_1.2000-1 libtinfo5_5.9-9 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5 libx11-6_2:1.5.0-1 libx11-data_2:1.5.0-1 libxau6_1:1.0.7-1 libxcb-render0_1.8.1-1 libxcb-shm0_1.8.1-1 libxcb1_1.8.1-1 libxcomposite1_1:0.4.3-2 libxcursor1_1:1.1.13-1 libxdamage1_1:1.1.3-2 libxdmcp6_1:1.1.1-1 libxext6_2:1.3.1-2 libxfixes3_1:5.0-4 libxft2_2.3.1-1 libxi6_2:1.6.1-1 libxinerama1_2:1.1.2-1 libxml2_2.8.0+dfsg1-4 libxrandr2_2:1.3.2-2 libxrender1_1:0.9.7-1 libxss1_1:1.2.2-1 linux-libc-dev_3.2.20-1 login_1:4.1.5.1-1 lsb-base_4.1+Debian7 make_3.81-8.2 man-db_2.6.2-1 mawk_1.3.3-17 mime-support_3.52-1 mount_2.20.1-5 multiarch-support_2.13-33 ncurses-base_5.9-9 ncurses-bin_5.9-9 passwd_1:4.1.5.1-1 patch_2.6.1-3 perl_5.14.2-12 perl-base_5.14.2-12 perl-modules_5.14.2-12 po-debconf_1.0.16+nmu2 python_2.7.3~rc2-1 python-all_2.7.3~rc2-1 python-all-dev_2.7.3~rc2-1 python-cairo_1.8.8-1+b2 python-cogent_1.5.1-2 python-dateutil_1.5-1 python-dev_2.7.3~rc2-1 python-docutils_0.8.1-7 python-gi_3.2.2-1 python-gobject_3.2.2-1 python-gobject-2_2.28.6-10 python-jinja2_2.6-1 python-markupsafe_0.15-1 python-matplotlib_1.1.1~rc2-1 python-matplotlib-data_1.1.1~rc2-1 python-minimal_2.7.3~rc2-1 python-numpy_1:1.6.2-1 python-pygments_1.5+dfsg-1 python-pyparsing_1.5.6+dfsg1-1 python-roman_0.8.1-7 python-sphinx_1.1.3+dfsg-4 python-support_1.0.14 python-tz_2012c-1 python2.6_2.6.7-4 python2.6-dev_2.6.7-4 python2.6-minimal_2.6.7-4 python2.7_2.7.3-1 python2.7-dev_2.7.3-1 python2.7-minimal_2.7.3-1 readline-common_6.2-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-qiime-dummy_0.invalid.0 sed_4.2.1-10 sensible-utils_0.0.7 sgml-base_1.26+nmu3 shared-mime-info_1.0-1 sphinx-common_1.1.3+dfsg-4 sysv-rc_2.88dsf-27 sysvinit_2.88dsf-27 sysvinit-utils_2.88dsf-27 tar_1.26-4 tcl8.5_8.5.11-2 tk8.5_8.5.11-2 ttf-dejavu-core_2.33-2 tzdata_2012c-1 ucf_3.0025+nmu3 util-linux_2.20.1-5 x11-common_1:7.6+13 xml-core_0.13+nmu1 xz-utils_5.1.1alpha+20120614-1 zlib1g_1:1.2.7.dfsg-13 zlib1g-dev_1:1.2.7.dfsg-13 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Tue May 22 07:55:18 2012 UTC using DSA key ID C09FD35A gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./qiime_1.5.0-1.dsc dpkg-source: info: extracting qiime in qiime-1.5.0 dpkg-source: info: unpacking qiime_1.5.0.orig.tar.gz dpkg-source: info: unpacking qiime_1.5.0-1.debian.tar.gz dpkg-source: info: applying python26_trim_sff_primers.patch dpkg-source: info: applying fix_binary_helper_location.patch Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── HOME=/sbuild-nonexistent LOGNAME=root PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/bin/X11 SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=0 SCHROOT_GROUP=root SCHROOT_SESSION_ID=unstable-amd64-sbuild-027338f0-fc07-4312-aa9f-f4357b9d7445 SCHROOT_UID=0 SCHROOT_USER=root SHELL=/bin/sh USER=root dpkg-buildpackage ───────────────── dpkg-buildpackage: warning: using a gain-root-command while being root dpkg-buildpackage: source package qiime dpkg-buildpackage: source version 1.5.0-1 dpkg-buildpackage: source changed by Andreas Tille dpkg-source --before-build qiime-1.5.0 dpkg-buildpackage: host architecture amd64 fakeroot debian/rules clean dh clean --with python2 dh_testdir dh_auto_clean make[1]: Entering directory `/«PKGBUILDDIR»/qiime/support_files/denoiser/FlowgramAlignment' ghc --make -O2 FlowgramAli_4frame [1 of 3] Compiling ADPCombinators ( ADPCombinators.lhs, ADPCombinators.o ) clang: warning: -Wl,--hash-size=31: 'linker' input unused when '-c' is present clang: warning: -Wl,--reduce-memory-overheads: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '-fno-stack-protector' clang: warning: argument unused during compilation: '-I .' [2 of 3] Compiling FlowgramUtils ( FlowgramUtils.lhs, FlowgramUtils.o ) clang: warning: -Wl,--hash-size=31: 'linker' input unused when '-c' is present clang: warning: -Wl,--reduce-memory-overheads: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '-fno-stack-protector' clang: warning: argument unused during compilation: '-I .' [3 of 3] Compiling Main ( FlowgramAli_4frame.lhs, FlowgramAli_4frame.o ) clang: warning: -Wl,--hash-size=31: 'linker' input unused when '-c' is present clang: warning: -Wl,--reduce-memory-overheads: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '-fno-stack-protector' clang: warning: argument unused during compilation: '-I .' Linking FlowgramAli_4frame ... clang: warning: -Wl,--hash-size=31: 'linker' input unused when '-c' is present clang: warning: -Wl,--reduce-memory-overheads: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Izh_static_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Czh_static_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Fzh_static_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Dzh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziPtr_Ptr_static_info' clang: warning: argument unused during compilation: '-u base_GHCziWord_Wzh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziInt_I8zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziInt_I16zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziInt_I32zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziInt_I64zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziWord_W8zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziWord_W16zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziWord_W32zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziWord_W64zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziStable_StablePtr_static_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Izh_con_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Czh_con_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Fzh_con_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Dzh_con_info' clang: warning: argument unused during compilation: '-u base_GHCziPtr_Ptr_con_info' clang: warning: argument unused during compilation: '-u base_GHCziPtr_FunPtr_con_info' clang: warning: argument unused during compilation: '-u base_GHCziStable_StablePtr_con_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_False_closure' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_True_closure' clang: warning: argument unused during compilation: '-u base_GHCziPack_unpackCString_closure' clang: warning: argument unused during compilation: '-u base_GHCziIOziException_stackOverflow_closure' clang: warning: argument unused during compilation: '-u base_GHCziIOziException_heapOverflow_closure' clang: warning: argument unused during compilation: '-u base_ControlziExceptionziBase_nonTermination_closure' clang: warning: argument unused during compilation: '-u base_GHCziIOziException_blockedIndefinitelyOnMVar_closure' clang: warning: argument unused during compilation: '-u base_GHCziIOziException_blockedIndefinitelyOnSTM_closure' clang: warning: argument unused during compilation: '-u base_ControlziExceptionziBase_nestedAtomically_closure' clang: warning: argument unused during compilation: '-u base_GHCziWeak_runFinalizzerBatch_closure' clang: warning: argument unused during compilation: '-u base_GHCziTopHandler_flushStdHandles_closure' clang: warning: argument unused during compilation: '-u base_GHCziTopHandler_runIO_closure' clang: warning: argument unused during compilation: '-u base_GHCziTopHandler_runNonIO_closure' clang: warning: argument unused during compilation: '-u base_GHCziConcziIO_ensureIOManagerIsRunning_closure' clang: warning: argument unused during compilation: '-u base_GHCziConcziSync_runSparks_closure' clang: warning: argument unused during compilation: '-u base_GHCziConcziSignal_runHandlers_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_exit_': (.text+0x49): undefined reference to `base_GHCziTopHandler_flushStdHandles_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x19b): undefined reference to `base_GHCziTopHandler_runIO_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1a5): undefined reference to `base_GHCziTopHandler_runNonIO_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1af): undefined reference to `base_GHCziTopHandler_flushStdHandles_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1b9): undefined reference to `base_GHCziWeak_runFinalizzerBatch_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1c3): undefined reference to `base_GHCziIOziException_stackOverflow_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1cd): undefined reference to `base_GHCziIOziException_heapOverflow_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1d7): undefined reference to `base_GHCziPack_unpackCString_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1e1): undefined reference to `base_GHCziIOziException_blockedIndefinitelyOnMVar_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1eb): undefined reference to `base_ControlziExceptionziBase_nonTermination_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1f5): undefined reference to `base_GHCziIOziException_blockedIndefinitelyOnSTM_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1ff): undefined reference to `base_ControlziExceptionziBase_nestedAtomically_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x209): undefined reference to `base_GHCziConcziSync_runSparks_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x213): undefined reference to `base_GHCziConcziIO_ensureIOManagerIsRunning_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x21d): undefined reference to `base_GHCziConcziSignal_runHandlers_closure' /usr/lib/ghc/libHSrts.a(Schedule.o): In function `scheduleWaitThread': (.text+0xed5): undefined reference to `base_ControlziExceptionziBase_nonTermination_closure' /usr/lib/ghc/libHSrts.a(Schedule.o): In function `resurrectThreads': (.text+0x1581): undefined reference to `base_ControlziExceptionziBase_nonTermination_closure' /usr/lib/ghc/libHSrts.a(Schedule.o): In function `resurrectThreads': (.text+0x15a1): undefined reference to `base_GHCziIOziException_blockedIndefinitelyOnSTM_closure' /usr/lib/ghc/libHSrts.a(Schedule.o): In function `resurrectThreads': (.text+0x15c1): undefined reference to `base_GHCziIOziException_blockedIndefinitelyOnMVar_closure' /usr/lib/ghc/libHSrts.a(Threads.o): In function `threadStackOverflow': (.text+0x6e1): undefined reference to `base_GHCziIOziException_stackOverflow_closure' /usr/lib/ghc/libHSrts.a(Weak.o): In function `scheduleFinalizers': (.text+0x1e2): undefined reference to `base_GHCziWeak_runFinalizzerBatch_closure' /usr/lib/ghc/libHSrts.a(Signals.o): In function `startSignalHandlers': (.text+0x7e2): undefined reference to `base_GHCziConcziSignal_runHandlers_closure' /usr/lib/ghc/libHSrts.a(PrimOps.o):(.text+0xfd8): undefined reference to `base_ControlziExceptionziBase_nestedAtomically_closure' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkInt16': (.text+0x72): undefined reference to `base_GHCziInt_I16zh_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkWord': (.text+0xd1): undefined reference to `base_GHCziWord_Wzh_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkWord8': (.text+0xf2): undefined reference to `base_GHCziWord_W8zh_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkWord16': (.text+0x111): undefined reference to `base_GHCziWord_W16zh_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkDouble': (.text+0x1a6): undefined reference to `ghczmprim_GHCziTypes_Dzh_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkStablePtr': (.text+0x1d1): undefined reference to `base_GHCziStable_StablePtr_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkFunPtr': (.text+0x211): undefined reference to `base_GHCziPtr_FunPtr_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkString': (.text+0x290): undefined reference to `base_GHCziPack_unpackCString_closure' clang: error: linker command failed with exit code 1 (use -v to see invocation) make[1]: *** [FlowgramAli_4frame] Error 1 make[1]: Leaving directory `/«PKGBUILDDIR»/qiime/support_files/denoiser/FlowgramAlignment' make[1]: Entering directory `/«PKGBUILDDIR»/qiime/support_files/denoiser/FlowgramAlignment' cp FlowgramAli_4frame ../bin/ cp: cannot stat `FlowgramAli_4frame': No such file or directory make[1]: *** [install] Error 1 make[1]: Leaving directory `/«PKGBUILDDIR»/qiime/support_files/denoiser/FlowgramAlignment' Denoiser built. running clean 'build/lib.linux-x86_64-2.6' does not exist -- can't clean it 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-2.6' does not exist -- can't clean it make[1]: Entering directory `/«PKGBUILDDIR»/doc' sphinx-build -b html -d _build/doctrees . _build/html Making output directory... Running Sphinx v1.1.3 loading pickled environment... not yet created building [html]: targets for 173 source files that are out of date updating environment: 173 added, 0 changed, 0 removed reading sources... [ 0%] developer/coding_guidelines reading sources... [ 1%] developer/index reading sources... [ 1%] developer/reporting_and_fixing_bugs reading sources... [ 2%] documentation/biom_format reading sources... [ 2%] documentation/file_formats reading sources... [ 3%] documentation/index reading sources... [ 4%] documentation/script_index reading sources... [ 4%] documentation/table_objects reading sources... [ 5%] index reading sources... [ 5%] install/index reading sources... [ 6%] install/install reading sources... [ 6%] install/qiime_config reading sources... [ 7%] install/ubuntu_install reading sources... [ 8%] install/upgrade reading sources... [ 8%] install/virtual_box reading sources... [ 9%] install/vm_ec2 reading sources... [ 9%] scripts/add_qiime_labels reading sources... [ 10%] scripts/add_taxa reading sources... [ 10%] scripts/adjust_seq_orientation reading sources... [ 11%] scripts/align_seqs reading sources... [ 12%] scripts/alpha_diversity reading sources... [ 12%] scripts/alpha_diversity_metrics reading sources... [ 13%] scripts/alpha_rarefaction reading sources... [ 13%] scripts/ampliconnoise reading sources... [ 14%] scripts/assign_taxonomy reading sources... [ 15%] scripts/beta_diversity reading sources... [ 15%] scripts/beta_diversity_metrics reading sources... [ 16%] scripts/beta_diversity_through_plots reading sources... [ 16%] scripts/beta_significance reading sources... [ 17%] scripts/blast_wrapper reading sources... [ 17%] scripts/categorized_dist_scatterplot reading sources... [ 18%] scripts/check_id_map reading sources... [ 19%] scripts/clean_raxml_parsimony_tree reading sources... [ 19%] scripts/cluster_quality reading sources... [ 20%] scripts/collate_alpha reading sources... [ 20%] scripts/compare_3d_plots reading sources... [ 21%] scripts/compare_alpha_diversity reading sources... [ 21%] scripts/compare_categories reading sources... [ 22%] scripts/compare_distance_matrices reading sources... [ 23%] scripts/conditional_uncovered_probability reading sources... [ 23%] scripts/consensus_tree reading sources... [ 24%] scripts/convert_fastaqual_to_fastq reading sources... [ 24%] scripts/convert_otu_table_to_unifrac_sample_mapping reading sources... [ 25%] scripts/convert_unifrac_sample_mapping_to_otu_table reading sources... [ 26%] scripts/core_qiime_analyses reading sources... [ 26%] scripts/count_seqs reading sources... [ 27%] scripts/cytoscape_usage reading sources... [ 27%] scripts/denoise_wrapper reading sources... [ 28%] scripts/denoiser reading sources... [ 28%] scripts/denoiser_preprocess reading sources... [ 29%] scripts/denoiser_worker reading sources... [ 30%] scripts/dissimilarity_mtx_stats reading sources... [ 30%] scripts/distance_matrix_from_mapping reading sources... [ 31%] scripts/exclude_seqs_by_blast reading sources... [ 31%] scripts/extract_seqs_by_sample_id reading sources... [ 32%] scripts/filter_alignment reading sources... [ 32%] scripts/filter_distance_matrix reading sources... [ 33%] scripts/filter_fasta reading sources... [ 34%] scripts/filter_otus_by_sample reading sources... [ 34%] scripts/filter_otus_from_otu_table reading sources... [ 35%] scripts/filter_samples_from_otu_table reading sources... [ 35%] scripts/filter_tree reading sources... [ 36%] scripts/fix_arb_fasta reading sources... [ 36%] scripts/identify_chimeric_seqs reading sources... [ 37%] scripts/identify_missing_files reading sources... [ 38%] scripts/index reading sources... [ 38%] scripts/inflate_denoiser_output reading sources... [ 39%] scripts/insert_seqs_into_tree reading sources... [ 39%] scripts/jackknifed_beta_diversity reading sources... [ 40%] scripts/make_2d_plots reading sources... [ 41%] scripts/make_3d_plots reading sources... [ 41%] scripts/make_bootstrapped_tree reading sources... [ 42%] scripts/make_distance_boxplots reading sources... [ 42%] scripts/make_distance_comparison_plots reading sources... [ 43%] scripts/make_distance_histograms reading sources... [ 43%] scripts/make_fastq reading sources... [ 44%] scripts/make_library_id_lists reading sources... [ 45%] scripts/make_otu_heatmap reading sources... [ 45%] scripts/make_otu_heatmap_html reading sources... [ 46%] scripts/make_otu_network reading sources... [ 46%] scripts/make_otu_table reading sources... [ 47%] scripts/make_per_library_sff reading sources... [ 47%] scripts/make_phylogeny reading sources... [ 48%] scripts/make_prefs_file reading sources... [ 49%] scripts/make_qiime_py_file reading sources... [ 49%] scripts/make_qiime_rst_file reading sources... [ 50%] scripts/make_rarefaction_plots reading sources... [ 50%] scripts/make_tep reading sources... [ 51%] scripts/merge_mapping_files reading sources... 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[ 82%] scripts/summarize_taxa_through_plots reading sources... [ 83%] scripts/supervised_learning reading sources... [ 83%] scripts/transform_coordinate_matrices reading sources... [ 84%] scripts/tree_compare reading sources... [ 84%] scripts/trflp_file_to_otu_table reading sources... [ 85%] scripts/trim_sff_primers reading sources... [ 86%] scripts/truncate_fasta_qual_files reading sources... [ 86%] scripts/truncate_reverse_primer reading sources... [ 87%] scripts/unweight_fasta reading sources... [ 87%] scripts/upgma_cluster reading sources... [ 88%] scripts/validate_demultiplexed_fasta reading sources... [ 89%] tutorials/category_comparison reading sources... [ 89%] tutorials/chaining_otu_pickers reading sources... [ 90%] tutorials/chimera_checking reading sources... [ 90%] tutorials/creating_distance_comparison_plots reading sources... [ 91%] tutorials/denoising_454_data reading sources... [ 91%] tutorials/distance_matrix_comparison reading sources... 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[100%] tutorials/working_with_aws /«PKGBUILDDIR»/doc/install/ubuntu_install.rst:22: WARNING: Literal block ends without a blank line; unexpected unindent. /«PKGBUILDDIR»/doc/tutorials/running_supervised_learning.rst:5: WARNING: Duplicate explicit target name: "link". /«PKGBUILDDIR»/doc/tutorials/usearch_quality_filter.rst:5: WARNING: Duplicate explicit target name: "otupipe". looking for now-outdated files... none found pickling environment... done /«PKGBUILDDIR»/doc/developer/index.rst:: WARNING: document isn't included in any toctree /«PKGBUILDDIR»/doc/documentation/index.rst:: WARNING: document isn't included in any toctree /«PKGBUILDDIR»/doc/install/index.rst:: WARNING: document isn't included in any toctree /«PKGBUILDDIR»/doc/scripts/index.rst:: WARNING: document isn't included in any toctree /«PKGBUILDDIR»/doc/tutorials/index.rst:: WARNING: document isn't included in any toctree checking consistency... done preparing documents... done writing output... 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[ 12%] scripts/alpha_diversity_metrics writing output... [ 13%] scripts/alpha_rarefaction writing output... [ 13%] scripts/ampliconnoise writing output... [ 14%] scripts/assign_taxonomy writing output... [ 15%] scripts/beta_diversity writing output... [ 15%] scripts/beta_diversity_metrics writing output... [ 16%] scripts/beta_diversity_through_plots writing output... [ 16%] scripts/beta_significance writing output... [ 17%] scripts/blast_wrapper writing output... [ 17%] scripts/categorized_dist_scatterplot writing output... [ 18%] scripts/check_id_map writing output... [ 19%] scripts/clean_raxml_parsimony_tree writing output... [ 19%] scripts/cluster_quality writing output... [ 20%] scripts/collate_alpha writing output... [ 20%] scripts/compare_3d_plots writing output... [ 21%] scripts/compare_alpha_diversity writing output... [ 21%] scripts/compare_categories writing output... [ 22%] scripts/compare_distance_matrices writing output... [ 23%] scripts/conditional_uncovered_probability writing output... [ 23%] scripts/consensus_tree writing output... [ 24%] scripts/convert_fastaqual_to_fastq writing output... [ 24%] scripts/convert_otu_table_to_unifrac_sample_mapping writing output... [ 25%] scripts/convert_unifrac_sample_mapping_to_otu_table writing output... [ 26%] scripts/core_qiime_analyses writing output... [ 26%] scripts/count_seqs writing output... [ 27%] scripts/cytoscape_usage writing output... [ 27%] scripts/denoise_wrapper writing output... [ 28%] scripts/denoiser writing output... [ 28%] scripts/denoiser_preprocess writing output... [ 29%] scripts/denoiser_worker writing output... [ 30%] scripts/dissimilarity_mtx_stats writing output... [ 30%] scripts/distance_matrix_from_mapping writing output... [ 31%] scripts/exclude_seqs_by_blast writing output... [ 31%] scripts/extract_seqs_by_sample_id writing output... [ 32%] scripts/filter_alignment writing output... 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[ 54%] scripts/neighbor_joining writing output... [ 54%] scripts/nmds writing output... [ 55%] scripts/otu_category_significance writing output... [ 56%] scripts/parallel_align_seqs_pynast writing output... [ 56%] scripts/parallel_alpha_diversity writing output... [ 57%] scripts/parallel_assign_taxonomy_blast writing output... [ 57%] scripts/parallel_assign_taxonomy_rdp writing output... [ 58%] scripts/parallel_beta_diversity writing output... [ 58%] scripts/parallel_blast writing output... [ 59%] scripts/parallel_identify_chimeric_seqs writing output... [ 60%] scripts/parallel_multiple_rarefactions writing output... [ 60%] scripts/parallel_pick_otus_blast writing output... [ 61%] scripts/parallel_pick_otus_uclust_ref writing output... [ 61%] scripts/per_library_stats writing output... [ 62%] scripts/pick_otus writing output... [ 63%] scripts/pick_otus_through_otu_table writing output... [ 63%] scripts/pick_reference_otus_through_otu_table writing output... [ 64%] scripts/pick_rep_set writing output... [ 64%] scripts/pick_subsampled_reference_otus_through_otu_table writing output... [ 65%] scripts/plot_rank_abundance_graph writing output... [ 65%] scripts/plot_semivariogram writing output... [ 66%] scripts/plot_taxa_summary writing output... [ 67%] scripts/poller writing output... [ 67%] scripts/poller_example writing output... [ 68%] scripts/pool_by_metadata writing output... [ 68%] scripts/preferences_file writing output... [ 69%] scripts/principal_coordinates writing output... [ 69%] scripts/print_qiime_config writing output... [ 70%] scripts/process_iseq writing output... [ 71%] scripts/process_qseq writing output... [ 71%] scripts/process_sff writing output... [ 72%] scripts/quality_scores_plot writing output... [ 72%] scripts/relatedness writing output... [ 73%] scripts/shared_phylotypes writing output... [ 73%] scripts/simsam writing output... [ 74%] scripts/single_rarefaction writing output... [ 75%] scripts/sort_otu_table writing output... [ 75%] scripts/split_fasta_on_sample_ids writing output... [ 76%] scripts/split_libraries writing output... [ 76%] scripts/split_libraries_fastq writing output... [ 77%] scripts/split_otu_table writing output... [ 78%] scripts/split_otu_table_by_taxonomy writing output... [ 78%] scripts/start_parallel_jobs writing output... [ 79%] scripts/start_parallel_jobs_sc writing output... [ 79%] scripts/start_parallel_jobs_torque writing output... [ 80%] scripts/submit_to_mgrast writing output... [ 80%] scripts/subsample_fasta writing output... [ 81%] scripts/summarize_otu_by_cat writing output... [ 82%] scripts/summarize_taxa writing output... [ 82%] scripts/summarize_taxa_through_plots writing output... [ 83%] scripts/supervised_learning writing output... [ 83%] scripts/transform_coordinate_matrices writing output... [ 84%] scripts/tree_compare writing output... [ 84%] scripts/trflp_file_to_otu_table writing output... [ 85%] scripts/trim_sff_primers writing output... [ 86%] scripts/truncate_fasta_qual_files writing output... [ 86%] scripts/truncate_reverse_primer writing output... [ 87%] scripts/unweight_fasta writing output... [ 87%] scripts/upgma_cluster writing output... [ 88%] scripts/validate_demultiplexed_fasta writing output... [ 89%] tutorials/category_comparison writing output... [ 89%] tutorials/chaining_otu_pickers writing output... [ 90%] tutorials/chimera_checking writing output... [ 90%] tutorials/creating_distance_comparison_plots writing output... [ 91%] tutorials/denoising_454_data writing output... [ 91%] tutorials/distance_matrix_comparison writing output... [ 92%] tutorials/filtering_contamination_otus writing output... [ 93%] tutorials/index writing output... [ 93%] tutorials/open_reference_illumina_processing writing output... [ 94%] tutorials/parallel_qiime writing output... [ 94%] tutorials/processing_18S_data writing output... [ 95%] tutorials/processing_illumina_data writing output... [ 95%] tutorials/procrustes_analysis writing output... [ 96%] tutorials/retraining_rdp writing output... [ 97%] tutorials/rtax writing output... [ 97%] tutorials/running_supervised_learning writing output... [ 98%] tutorials/tutorial writing output... [ 98%] tutorials/unix_commands writing output... [ 99%] tutorials/usearch_quality_filter writing output... [100%] tutorials/working_with_aws writing additional files... genindex search copying images... [ 3%] tutorials/../images/taxheatmap.png copying images... [ 6%] tutorials/../images/pcoa1.png copying images... [ 9%] tutorials/../images/areachart1.png copying images... [ 12%] tutorials/../images/barchart1.png copying images... [ 15%] tutorials/../images/jackpcoa.png copying images... [ 18%] tutorials/../images/cyberduck_open_connection.png copying images... [ 21%] tutorials/../images/tree.png copying images... [ 24%] tutorials/../images/public_dns_entry.png copying images... [ 27%] tutorials/../images/time_comparisons2.png copying images... [ 30%] tutorials/../images/biplot.png copying images... [ 33%] tutorials/../images/cyberduck_opened_connection.png copying images... [ 36%] tutorials/../images/cyberduck_view_file.png copying images... [ 39%] tutorials/../images/example_primer_construct.png copying images... [ 42%] tutorials/../images/distance_boxplots1.png copying images... [ 45%] tutorials/../images/cyberduck_drag_and_drop_output_file.png copying images... [ 48%] tutorials/../images/network.png copying images... [ 51%] tutorials/../images/configure_ebs_volume_creation.png copying images... [ 54%] tutorials/../images/time_comparisons3.png copying images... [ 57%] tutorials/../images/time_comparisons1.png copying images... [ 60%] tutorials/../images/pcoa2.png copying images... [ 63%] tutorials/../images/procrustes_tutorial_figure1.png copying images... [ 66%] tutorials/../images/create_an_ebs_volume.png copying images... [ 69%] tutorials/../images/heatmap.png copying images... [ 72%] tutorials/../images/rarecurve.png copying images... [ 75%] tutorials/../images/configure_ebs_volume_attachment.png copying images... [ 78%] tutorials/../images/stop_instance.png copying images... [ 81%] tutorials/../images/mantel_correlogram.png copying images... [ 84%] tutorials/../images/fisheyeheatmap.png copying images... [ 87%] tutorials/../images/cyberduck_drag_and_drop_input_file.png copying images... [ 90%] tutorials/../images/cyberduck_create_output_file.png copying images... [ 93%] tutorials/../images/hist.png copying images... [ 96%] tutorials/../images/boottree.png copying images... [100%] tutorials/../images/UPGMAbytreatment.png copying static files... done dumping search index... done dumping object inventory... done build succeeded, 8 warnings. Build finished. The HTML pages are in _build/html. make[1]: Leaving directory `/«PKGBUILDDIR»/doc' Local documentation built with Sphinx. Open to following path with a web browser: /«PKGBUILDDIR»/doc/_build/html/index.html make[1]: Entering directory `/«PKGBUILDDIR»/qiime/support_files/denoiser/FlowgramAlignment' ghc --make -O2 FlowgramAli_4frame Linking FlowgramAli_4frame ... clang: warning: -Wl,--hash-size=31: 'linker' input unused when '-c' is present clang: warning: -Wl,--reduce-memory-overheads: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Izh_static_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Czh_static_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Fzh_static_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Dzh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziPtr_Ptr_static_info' clang: warning: argument unused during compilation: '-u base_GHCziWord_Wzh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziInt_I8zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziInt_I16zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziInt_I32zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziInt_I64zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziWord_W8zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziWord_W16zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziWord_W32zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziWord_W64zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziStable_StablePtr_static_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Izh_con_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Czh_con_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Fzh_con_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Dzh_con_info' clang: warning: argument unused during compilation: '-u base_GHCziPtr_Ptr_con_info' clang: warning: argument unused during compilation: '-u base_GHCziPtr_FunPtr_con_info' clang: warning: argument unused during compilation: '-u base_GHCziStable_StablePtr_con_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_False_closure' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_True_closure' clang: warning: argument unused during compilation: '-u base_GHCziPack_unpackCString_closure' clang: warning: argument unused during compilation: '-u base_GHCziIOziException_stackOverflow_closure' clang: warning: argument unused during compilation: '-u base_GHCziIOziException_heapOverflow_closure' clang: warning: argument unused during compilation: '-u base_ControlziExceptionziBase_nonTermination_closure' clang: warning: argument unused during compilation: '-u base_GHCziIOziException_blockedIndefinitelyOnMVar_closure' clang: warning: argument unused during compilation: '-u base_GHCziIOziException_blockedIndefinitelyOnSTM_closure' clang: warning: argument unused during compilation: '-u base_ControlziExceptionziBase_nestedAtomically_closure' clang: warning: argument unused during compilation: '-u base_GHCziWeak_runFinalizzerBatch_closure' clang: warning: argument unused during compilation: '-u base_GHCziTopHandler_flushStdHandles_closure' clang: warning: argument unused during compilation: '-u base_GHCziTopHandler_runIO_closure' clang: warning: argument unused during compilation: '-u base_GHCziTopHandler_runNonIO_closure' clang: warning: argument unused during compilation: '-u base_GHCziConcziIO_ensureIOManagerIsRunning_closure' clang: warning: argument unused during compilation: '-u base_GHCziConcziSync_runSparks_closure' clang: warning: argument unused during compilation: '-u base_GHCziConcziSignal_runHandlers_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_exit_': (.text+0x49): undefined reference to `base_GHCziTopHandler_flushStdHandles_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x19b): undefined reference to `base_GHCziTopHandler_runIO_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1a5): undefined reference to `base_GHCziTopHandler_runNonIO_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1af): undefined reference to `base_GHCziTopHandler_flushStdHandles_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1b9): undefined reference to `base_GHCziWeak_runFinalizzerBatch_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1c3): undefined reference to `base_GHCziIOziException_stackOverflow_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1cd): undefined reference to `base_GHCziIOziException_heapOverflow_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1d7): undefined reference to `base_GHCziPack_unpackCString_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1e1): undefined reference to `base_GHCziIOziException_blockedIndefinitelyOnMVar_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1eb): undefined reference to `base_ControlziExceptionziBase_nonTermination_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1f5): undefined reference to `base_GHCziIOziException_blockedIndefinitelyOnSTM_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1ff): undefined reference to `base_ControlziExceptionziBase_nestedAtomically_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x209): undefined reference to `base_GHCziConcziSync_runSparks_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x213): undefined reference to `base_GHCziConcziIO_ensureIOManagerIsRunning_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x21d): undefined reference to `base_GHCziConcziSignal_runHandlers_closure' /usr/lib/ghc/libHSrts.a(Schedule.o): In function `scheduleWaitThread': (.text+0xed5): undefined reference to `base_ControlziExceptionziBase_nonTermination_closure' /usr/lib/ghc/libHSrts.a(Schedule.o): In function `resurrectThreads': (.text+0x1581): undefined reference to `base_ControlziExceptionziBase_nonTermination_closure' /usr/lib/ghc/libHSrts.a(Schedule.o): In function `resurrectThreads': (.text+0x15a1): undefined reference to `base_GHCziIOziException_blockedIndefinitelyOnSTM_closure' /usr/lib/ghc/libHSrts.a(Schedule.o): In function `resurrectThreads': (.text+0x15c1): undefined reference to `base_GHCziIOziException_blockedIndefinitelyOnMVar_closure' /usr/lib/ghc/libHSrts.a(Threads.o): In function `threadStackOverflow': (.text+0x6e1): undefined reference to `base_GHCziIOziException_stackOverflow_closure' /usr/lib/ghc/libHSrts.a(Weak.o): In function `scheduleFinalizers': (.text+0x1e2): undefined reference to `base_GHCziWeak_runFinalizzerBatch_closure' /usr/lib/ghc/libHSrts.a(Signals.o): In function `startSignalHandlers': (.text+0x7e2): undefined reference to `base_GHCziConcziSignal_runHandlers_closure' /usr/lib/ghc/libHSrts.a(PrimOps.o):(.text+0xfd8): undefined reference to `base_ControlziExceptionziBase_nestedAtomically_closure' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkInt16': (.text+0x72): undefined reference to `base_GHCziInt_I16zh_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkWord': (.text+0xd1): undefined reference to `base_GHCziWord_Wzh_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkWord8': (.text+0xf2): undefined reference to `base_GHCziWord_W8zh_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkWord16': (.text+0x111): undefined reference to `base_GHCziWord_W16zh_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkDouble': (.text+0x1a6): undefined reference to `ghczmprim_GHCziTypes_Dzh_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkStablePtr': (.text+0x1d1): undefined reference to `base_GHCziStable_StablePtr_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkFunPtr': (.text+0x211): undefined reference to `base_GHCziPtr_FunPtr_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkString': (.text+0x290): undefined reference to `base_GHCziPack_unpackCString_closure' clang: error: linker command failed with exit code 1 (use -v to see invocation) make[1]: *** [FlowgramAli_4frame] Error 1 make[1]: Leaving directory `/«PKGBUILDDIR»/qiime/support_files/denoiser/FlowgramAlignment' make[1]: Entering directory `/«PKGBUILDDIR»/qiime/support_files/denoiser/FlowgramAlignment' cp FlowgramAli_4frame ../bin/ cp: cannot stat `FlowgramAli_4frame': No such file or directory make[1]: *** [install] Error 1 make[1]: Leaving directory `/«PKGBUILDDIR»/qiime/support_files/denoiser/FlowgramAlignment' Denoiser built. running clean 'build/lib.linux-x86_64-2.7' does not exist -- can't clean it 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-2.7' does not exist -- can't clean it make[1]: Entering directory `/«PKGBUILDDIR»/doc' sphinx-build -b html -d _build/doctrees . _build/html Running Sphinx v1.1.3 loading pickled environment... done building [html]: targets for 0 source files that are out of date updating environment: 0 added, 0 changed, 0 removed looking for now-outdated files... none found no targets are out of date. Build finished. The HTML pages are in _build/html. make[1]: Leaving directory `/«PKGBUILDDIR»/doc' Local documentation built with Sphinx. Open to following path with a web browser: /«PKGBUILDDIR»/doc/_build/html/index.html debian/rules override_dh_clean make[1]: Entering directory `/«PKGBUILDDIR»' dh_clean rm -rf doc/_build ( cd qiime/support_files/denoiser/FlowgramAlignment && make clean ) || true make[2]: Entering directory `/«PKGBUILDDIR»/qiime/support_files/denoiser/FlowgramAlignment' rm *.o rm *.hi rm FlowgramAli_4frame rm: cannot remove `FlowgramAli_4frame': No such file or directory make[2]: *** [clean] Error 1 make[2]: Leaving directory `/«PKGBUILDDIR»/qiime/support_files/denoiser/FlowgramAlignment' rm -f qiime/support_files/denoiser/bin/* make[1]: Leaving directory `/«PKGBUILDDIR»' debian/rules build-arch dh build-arch --with python2 dh_testdir -a dh_auto_configure -a dh_auto_build -a make[1]: Entering directory `/«PKGBUILDDIR»/qiime/support_files/denoiser/FlowgramAlignment' ghc --make -O2 FlowgramAli_4frame [1 of 3] Compiling ADPCombinators ( ADPCombinators.lhs, ADPCombinators.o ) clang: warning: -Wl,--hash-size=31: 'linker' input unused when '-c' is present clang: warning: -Wl,--reduce-memory-overheads: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '-fno-stack-protector' clang: warning: argument unused during compilation: '-I .' [2 of 3] Compiling FlowgramUtils ( FlowgramUtils.lhs, FlowgramUtils.o ) clang: warning: -Wl,--hash-size=31: 'linker' input unused when '-c' is present clang: warning: -Wl,--reduce-memory-overheads: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '-fno-stack-protector' clang: warning: argument unused during compilation: '-I .' [3 of 3] Compiling Main ( FlowgramAli_4frame.lhs, FlowgramAli_4frame.o ) clang: warning: -Wl,--hash-size=31: 'linker' input unused when '-c' is present clang: warning: -Wl,--reduce-memory-overheads: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '-fno-stack-protector' clang: warning: argument unused during compilation: '-I .' Linking FlowgramAli_4frame ... clang: warning: -Wl,--hash-size=31: 'linker' input unused when '-c' is present clang: warning: -Wl,--reduce-memory-overheads: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Izh_static_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Czh_static_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Fzh_static_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Dzh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziPtr_Ptr_static_info' clang: warning: argument unused during compilation: '-u base_GHCziWord_Wzh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziInt_I8zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziInt_I16zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziInt_I32zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziInt_I64zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziWord_W8zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziWord_W16zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziWord_W32zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziWord_W64zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziStable_StablePtr_static_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Izh_con_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Czh_con_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Fzh_con_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Dzh_con_info' clang: warning: argument unused during compilation: '-u base_GHCziPtr_Ptr_con_info' clang: warning: argument unused during compilation: '-u base_GHCziPtr_FunPtr_con_info' clang: warning: argument unused during compilation: '-u base_GHCziStable_StablePtr_con_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_False_closure' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_True_closure' clang: warning: argument unused during compilation: '-u base_GHCziPack_unpackCString_closure' clang: warning: argument unused during compilation: '-u base_GHCziIOziException_stackOverflow_closure' clang: warning: argument unused during compilation: '-u base_GHCziIOziException_heapOverflow_closure' clang: warning: argument unused during compilation: '-u base_ControlziExceptionziBase_nonTermination_closure' clang: warning: argument unused during compilation: '-u base_GHCziIOziException_blockedIndefinitelyOnMVar_closure' clang: warning: argument unused during compilation: '-u base_GHCziIOziException_blockedIndefinitelyOnSTM_closure' clang: warning: argument unused during compilation: '-u base_ControlziExceptionziBase_nestedAtomically_closure' clang: warning: argument unused during compilation: '-u base_GHCziWeak_runFinalizzerBatch_closure' clang: warning: argument unused during compilation: '-u base_GHCziTopHandler_flushStdHandles_closure' clang: warning: argument unused during compilation: '-u base_GHCziTopHandler_runIO_closure' clang: warning: argument unused during compilation: '-u base_GHCziTopHandler_runNonIO_closure' clang: warning: argument unused during compilation: '-u base_GHCziConcziIO_ensureIOManagerIsRunning_closure' clang: warning: argument unused during compilation: '-u base_GHCziConcziSync_runSparks_closure' clang: warning: argument unused during compilation: '-u base_GHCziConcziSignal_runHandlers_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_exit_': (.text+0x49): undefined reference to `base_GHCziTopHandler_flushStdHandles_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x19b): undefined reference to `base_GHCziTopHandler_runIO_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1a5): undefined reference to `base_GHCziTopHandler_runNonIO_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1af): undefined reference to `base_GHCziTopHandler_flushStdHandles_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1b9): undefined reference to `base_GHCziWeak_runFinalizzerBatch_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1c3): undefined reference to `base_GHCziIOziException_stackOverflow_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1cd): undefined reference to `base_GHCziIOziException_heapOverflow_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1d7): undefined reference to `base_GHCziPack_unpackCString_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1e1): undefined reference to `base_GHCziIOziException_blockedIndefinitelyOnMVar_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1eb): undefined reference to `base_ControlziExceptionziBase_nonTermination_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1f5): undefined reference to `base_GHCziIOziException_blockedIndefinitelyOnSTM_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1ff): undefined reference to `base_ControlziExceptionziBase_nestedAtomically_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x209): undefined reference to `base_GHCziConcziSync_runSparks_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x213): undefined reference to `base_GHCziConcziIO_ensureIOManagerIsRunning_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x21d): undefined reference to `base_GHCziConcziSignal_runHandlers_closure' /usr/lib/ghc/libHSrts.a(Schedule.o): In function `scheduleWaitThread': (.text+0xed5): undefined reference to `base_ControlziExceptionziBase_nonTermination_closure' /usr/lib/ghc/libHSrts.a(Schedule.o): In function `resurrectThreads': (.text+0x1581): undefined reference to `base_ControlziExceptionziBase_nonTermination_closure' /usr/lib/ghc/libHSrts.a(Schedule.o): In function `resurrectThreads': (.text+0x15a1): undefined reference to `base_GHCziIOziException_blockedIndefinitelyOnSTM_closure' /usr/lib/ghc/libHSrts.a(Schedule.o): In function `resurrectThreads': (.text+0x15c1): undefined reference to `base_GHCziIOziException_blockedIndefinitelyOnMVar_closure' /usr/lib/ghc/libHSrts.a(Threads.o): In function `threadStackOverflow': (.text+0x6e1): undefined reference to `base_GHCziIOziException_stackOverflow_closure' /usr/lib/ghc/libHSrts.a(Weak.o): In function `scheduleFinalizers': (.text+0x1e2): undefined reference to `base_GHCziWeak_runFinalizzerBatch_closure' /usr/lib/ghc/libHSrts.a(Signals.o): In function `startSignalHandlers': (.text+0x7e2): undefined reference to `base_GHCziConcziSignal_runHandlers_closure' /usr/lib/ghc/libHSrts.a(PrimOps.o):(.text+0xfd8): undefined reference to `base_ControlziExceptionziBase_nestedAtomically_closure' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkInt16': (.text+0x72): undefined reference to `base_GHCziInt_I16zh_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkWord': (.text+0xd1): undefined reference to `base_GHCziWord_Wzh_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkWord8': (.text+0xf2): undefined reference to `base_GHCziWord_W8zh_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkWord16': (.text+0x111): undefined reference to `base_GHCziWord_W16zh_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkDouble': (.text+0x1a6): undefined reference to `ghczmprim_GHCziTypes_Dzh_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkStablePtr': (.text+0x1d1): undefined reference to `base_GHCziStable_StablePtr_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkFunPtr': (.text+0x211): undefined reference to `base_GHCziPtr_FunPtr_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkString': (.text+0x290): undefined reference to `base_GHCziPack_unpackCString_closure' clang: error: linker command failed with exit code 1 (use -v to see invocation) make[1]: *** [FlowgramAli_4frame] Error 1 make[1]: Leaving directory `/«PKGBUILDDIR»/qiime/support_files/denoiser/FlowgramAlignment' make[1]: Entering directory `/«PKGBUILDDIR»/qiime/support_files/denoiser/FlowgramAlignment' cp FlowgramAli_4frame ../bin/ cp: cannot stat `FlowgramAli_4frame': No such file or directory make[1]: *** [install] Error 1 make[1]: Leaving directory `/«PKGBUILDDIR»/qiime/support_files/denoiser/FlowgramAlignment' Denoiser built. running build running build_py creating build creating build/lib.linux-x86_64-2.6 creating build/lib.linux-x86_64-2.6/qiime copying qiime/trim_sff_primers.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/collate_alpha.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/supervised_learning.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/tree_compare.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/simsam.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/test.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/convert_fastaqual_to_fastq.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/truncate_fasta_qual_files.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/process_sff.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/validate_demultiplexed_fasta.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/identify_chimeric_seqs.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/sort.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/make_3d_plots.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/truncate_reverse_primer.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/conditional_uncovered_probability.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/compare_alpha_diversity.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/check_id_map.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/make_phylogeny.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/pick_subsampled_reference_otus_through_otu_table.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/denoise_wrapper.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/util.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/golay.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/pick_rep_set.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/categorized_dist_scatterplot.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/shared_phylotypes.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/plot_rank_abundance_graph.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/split.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/make_library_id_lists.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/plot_semivariogram.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/make_per_library_sff.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/clean_raxml_parsimony_tree.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/make_otu_heatmap_html.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/hierarchical_cluster.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/nmds.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/pick_otus.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/principal_coordinates.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/biplots.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/quality.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/cluster_quality.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/summarize_taxa.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/colors.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/workflow.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/transform_coordinate_matrices.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/filter_otus_by_sample.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/distance_matrix_from_mapping.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/longitudinal_otu_category_significance.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/merge_mapping_files.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/make_bootstrapped_tree.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/make_rarefaction_plots.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/make_2d_plots.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/__init__.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/group.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/filter_alignment.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/make_distance_histograms.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/assign_taxonomy.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/alpha_diversity.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/filter.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/make_otu_heatmap.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/make_fastq.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/make_otu_network.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/plot_taxa_summary.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/otu_category_significance.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/split_libraries_fastq.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/make_otu_table.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/format.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/rarefaction.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/split_libraries.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/quality_scores_plot.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/compare_distance_matrices.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/insert_seqs_into_tree.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/exclude_seqs_by_blast.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/relatedness_library.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/beta_metrics.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/adjust_seq_orientation.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/submit_to_mgrast.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/add_qiime_labels.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/beta_diversity.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/hamming.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/stats.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/align_seqs.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/parse.py -> build/lib.linux-x86_64-2.6/qiime copying qiime/barcode.py -> build/lib.linux-x86_64-2.6/qiime creating build/lib.linux-x86_64-2.6/qiime/parallel copying qiime/parallel/assign_taxonomy_blast.py -> build/lib.linux-x86_64-2.6/qiime/parallel copying qiime/parallel/pick_otus_uclust_ref.py -> build/lib.linux-x86_64-2.6/qiime/parallel copying qiime/parallel/blast.py -> build/lib.linux-x86_64-2.6/qiime/parallel copying qiime/parallel/multiple_rarefactions.py -> build/lib.linux-x86_64-2.6/qiime/parallel copying qiime/parallel/identify_chimeric_seqs.py -> build/lib.linux-x86_64-2.6/qiime/parallel copying qiime/parallel/pick_otus_blast.py -> build/lib.linux-x86_64-2.6/qiime/parallel copying qiime/parallel/util.py -> build/lib.linux-x86_64-2.6/qiime/parallel copying qiime/parallel/poller.py -> build/lib.linux-x86_64-2.6/qiime/parallel copying qiime/parallel/assign_taxonomy_rdp.py -> build/lib.linux-x86_64-2.6/qiime/parallel copying qiime/parallel/__init__.py -> build/lib.linux-x86_64-2.6/qiime/parallel copying qiime/parallel/alpha_diversity.py -> build/lib.linux-x86_64-2.6/qiime/parallel copying qiime/parallel/align_seqs_pynast.py -> build/lib.linux-x86_64-2.6/qiime/parallel copying qiime/parallel/beta_diversity.py -> build/lib.linux-x86_64-2.6/qiime/parallel creating build/lib.linux-x86_64-2.6/qiime/pycogent_backports copying qiime/pycogent_backports/tree.py -> build/lib.linux-x86_64-2.6/qiime/pycogent_backports copying qiime/pycogent_backports/muscle.py -> build/lib.linux-x86_64-2.6/qiime/pycogent_backports copying qiime/pycogent_backports/raxml_v730.py -> build/lib.linux-x86_64-2.6/qiime/pycogent_backports copying qiime/pycogent_backports/rtax.py -> build/lib.linux-x86_64-2.6/qiime/pycogent_backports copying qiime/pycogent_backports/parsinsert.py -> build/lib.linux-x86_64-2.6/qiime/pycogent_backports copying qiime/pycogent_backports/uclust.py -> build/lib.linux-x86_64-2.6/qiime/pycogent_backports copying qiime/pycogent_backports/rdp_classifier.py -> build/lib.linux-x86_64-2.6/qiime/pycogent_backports copying qiime/pycogent_backports/mothur.py -> build/lib.linux-x86_64-2.6/qiime/pycogent_backports copying qiime/pycogent_backports/pplacer.py -> build/lib.linux-x86_64-2.6/qiime/pycogent_backports copying qiime/pycogent_backports/usearch.py -> build/lib.linux-x86_64-2.6/qiime/pycogent_backports copying qiime/pycogent_backports/__init__.py -> build/lib.linux-x86_64-2.6/qiime/pycogent_backports copying qiime/pycogent_backports/guppy.py -> build/lib.linux-x86_64-2.6/qiime/pycogent_backports copying qiime/pycogent_backports/distribution_plots.py -> build/lib.linux-x86_64-2.6/qiime/pycogent_backports creating build/lib.linux-x86_64-2.6/qiime/denoiser copying qiime/denoiser/utils.py -> build/lib.linux-x86_64-2.6/qiime/denoiser copying qiime/denoiser/denoise_worker.py -> build/lib.linux-x86_64-2.6/qiime/denoiser copying qiime/denoiser/denoise_postprocess.py -> build/lib.linux-x86_64-2.6/qiime/denoiser copying qiime/denoiser/flowgram_filter.py -> build/lib.linux-x86_64-2.6/qiime/denoiser copying qiime/denoiser/flowgram_clustering.py -> build/lib.linux-x86_64-2.6/qiime/denoiser copying qiime/denoiser/__init__.py -> build/lib.linux-x86_64-2.6/qiime/denoiser copying qiime/denoiser/preprocess.py -> build/lib.linux-x86_64-2.6/qiime/denoiser copying qiime/denoiser/make_cluster_jobs.py -> build/lib.linux-x86_64-2.6/qiime/denoiser copying qiime/denoiser/cluster_utils.py -> build/lib.linux-x86_64-2.6/qiime/denoiser creating build/lib.linux-x86_64-2.6/qiime/support_files copying qiime/support_files/qiime_config -> build/lib.linux-x86_64-2.6/qiime/support_files creating build/lib.linux-x86_64-2.6/qiime/support_files/css copying qiime/support_files/css/qiime_style.css -> build/lib.linux-x86_64-2.6/qiime/support_files/css creating build/lib.linux-x86_64-2.6/qiime/support_files/images copying qiime/support_files/images/qiime_header.png -> build/lib.linux-x86_64-2.6/qiime/support_files/images creating build/lib.linux-x86_64-2.6/qiime/support_files/js copying qiime/support_files/js/jquery.tablednd_0_5.js -> build/lib.linux-x86_64-2.6/qiime/support_files/js copying qiime/support_files/js/jquery.js -> build/lib.linux-x86_64-2.6/qiime/support_files/js copying qiime/support_files/js/histograms.js -> build/lib.linux-x86_64-2.6/qiime/support_files/js copying qiime/support_files/js/otu_count_display.js -> build/lib.linux-x86_64-2.6/qiime/support_files/js copying qiime/support_files/js/overlib.js -> build/lib.linux-x86_64-2.6/qiime/support_files/js creating build/lib.linux-x86_64-2.6/qiime/support_files/R copying qiime/support_files/R/loaddata.r -> build/lib.linux-x86_64-2.6/qiime/support_files/R copying qiime/support_files/R/util.r -> build/lib.linux-x86_64-2.6/qiime/support_files/R copying qiime/support_files/R/randomforests_util.r -> build/lib.linux-x86_64-2.6/qiime/support_files/R copying qiime/support_files/R/randomforests.r -> build/lib.linux-x86_64-2.6/qiime/support_files/R copying qiime/support_files/R/rda.r -> build/lib.linux-x86_64-2.6/qiime/support_files/R copying qiime/support_files/R/mrpp.r -> build/lib.linux-x86_64-2.6/qiime/support_files/R copying qiime/support_files/R/morans_i.r -> build/lib.linux-x86_64-2.6/qiime/support_files/R copying qiime/support_files/R/betadisper.r -> build/lib.linux-x86_64-2.6/qiime/support_files/R copying qiime/support_files/R/adonis.r -> build/lib.linux-x86_64-2.6/qiime/support_files/R creating build/lib.linux-x86_64-2.6/qiime/support_files/denoiser creating build/lib.linux-x86_64-2.6/qiime/support_files/denoiser/Data copying qiime/support_files/denoiser/Data/FLX_error_profile.dat -> build/lib.linux-x86_64-2.6/qiime/support_files/denoiser/Data copying qiime/support_files/denoiser/Data/Titanium_error_profile.dat -> build/lib.linux-x86_64-2.6/qiime/support_files/denoiser/Data copying qiime/support_files/denoiser/Data/probabilities.txt -> build/lib.linux-x86_64-2.6/qiime/support_files/denoiser/Data creating build/lib.linux-x86_64-2.6/qiime/support_files/denoiser/TestData copying qiime/support_files/denoiser/TestData/test_flow_file.dat -> build/lib.linux-x86_64-2.6/qiime/support_files/denoiser/TestData copying qiime/support_files/denoiser/TestData/denoiser_test_set.sff.txt -> build/lib.linux-x86_64-2.6/qiime/support_files/denoiser/TestData copying qiime/support_files/denoiser/TestData/tiny_test.sff.txt -> build/lib.linux-x86_64-2.6/qiime/support_files/denoiser/TestData copying qiime/support_files/denoiser/TestData/test_set_seqs.fna -> build/lib.linux-x86_64-2.6/qiime/support_files/denoiser/TestData running build_scripts creating build/scripts-2.6 copying and adjusting scripts/collate_alpha.py -> build/scripts-2.6 copying and adjusting scripts/supervised_learning.py -> build/scripts-2.6 copying and adjusting scripts/tree_compare.py -> build/scripts-2.6 copying and adjusting scripts/make_prefs_file.py -> build/scripts-2.6 copying and adjusting scripts/dissimilarity_mtx_stats.py -> build/scripts-2.6 copying and adjusting scripts/single_rarefaction.py -> build/scripts-2.6 copying and adjusting scripts/simsam.py -> build/scripts-2.6 copying and adjusting scripts/convert_fastaqual_to_fastq.py -> build/scripts-2.6 copying and adjusting scripts/truncate_fasta_qual_files.py -> build/scripts-2.6 copying and adjusting scripts/process_sff.py -> build/scripts-2.6 copying and adjusting scripts/relatedness.py -> build/scripts-2.6 copying and adjusting scripts/make_tep.py -> build/scripts-2.6 copying and adjusting scripts/multiple_rarefactions.py -> build/scripts-2.6 copying and adjusting scripts/validate_demultiplexed_fasta.py -> build/scripts-2.6 copying and adjusting scripts/parallel_blast.py -> build/scripts-2.6 copying and adjusting scripts/identify_chimeric_seqs.py -> build/scripts-2.6 copying and adjusting scripts/summarize_taxa_through_plots.py -> build/scripts-2.6 copying and adjusting scripts/denoiser_preprocess.py -> build/scripts-2.6 copying and adjusting scripts/make_3d_plots.py -> build/scripts-2.6 copying and adjusting scripts/truncate_reverse_primer.py -> build/scripts-2.6 copying and adjusting scripts/conditional_uncovered_probability.py -> build/scripts-2.6 copying and adjusting scripts/parallel_alpha_diversity.py -> build/scripts-2.6 copying and adjusting scripts/compare_alpha_diversity.py -> build/scripts-2.6 copying and adjusting scripts/check_id_map.py -> build/scripts-2.6 copying and adjusting scripts/blast_wrapper.py -> build/scripts-2.6 copying and adjusting scripts/neighbor_joining.py -> build/scripts-2.6 copying and adjusting scripts/make_phylogeny.py -> build/scripts-2.6 copying and adjusting scripts/fix_arb_fasta.py -> build/scripts-2.6 copying and adjusting scripts/pick_subsampled_reference_otus_through_otu_table.py -> build/scripts-2.6 copying and adjusting scripts/core_qiime_analyses.py -> build/scripts-2.6 copying and adjusting scripts/make_distance_comparison_plots.py -> build/scripts-2.6 copying and adjusting scripts/denoise_wrapper.py -> build/scripts-2.6 copying and adjusting scripts/pick_rep_set.py -> build/scripts-2.6 copying and adjusting scripts/categorized_dist_scatterplot.py -> build/scripts-2.6 copying and adjusting scripts/ampliconnoise.py -> build/scripts-2.6 copying and adjusting scripts/shared_phylotypes.py -> build/scripts-2.6 copying and adjusting scripts/poller.py -> build/scripts-2.6 copying and adjusting scripts/beta_diversity_through_plots.py -> build/scripts-2.6 copying and adjusting scripts/plot_rank_abundance_graph.py -> build/scripts-2.6 copying and adjusting scripts/convert_otu_table_to_unifrac_sample_mapping.py -> build/scripts-2.6 copying and adjusting scripts/start_parallel_jobs_torque.py -> build/scripts-2.6 copying and adjusting scripts/make_library_id_lists.py -> build/scripts-2.6 copying and adjusting scripts/pick_otus_through_otu_table.py -> build/scripts-2.6 copying and adjusting scripts/make_qiime_py_file.py -> build/scripts-2.6 copying and adjusting scripts/plot_semivariogram.py -> build/scripts-2.6 copying and adjusting scripts/merge_otu_tables.py -> build/scripts-2.6 copying and adjusting scripts/make_per_library_sff.py -> build/scripts-2.6 copying and adjusting scripts/clean_raxml_parsimony_tree.py -> build/scripts-2.6 copying and adjusting scripts/make_qiime_rst_file.py -> build/scripts-2.6 copying and adjusting scripts/sort_otu_table.py -> build/scripts-2.6 copying and adjusting scripts/add_taxa.py -> build/scripts-2.6 copying and adjusting scripts/start_parallel_jobs.py -> build/scripts-2.6 copying and adjusting scripts/parallel_identify_chimeric_seqs.py -> build/scripts-2.6 copying and adjusting scripts/make_otu_heatmap_html.py -> build/scripts-2.6 copying and adjusting scripts/filter_otus_from_otu_table.py -> build/scripts-2.6 copying and adjusting scripts/parallel_assign_taxonomy_blast.py -> build/scripts-2.6 copying and adjusting scripts/nmds.py -> build/scripts-2.6 copying and adjusting scripts/pick_otus.py -> build/scripts-2.6 copying and adjusting scripts/process_qseq.py -> build/scripts-2.6 copying and adjusting scripts/principal_coordinates.py -> build/scripts-2.6 copying and adjusting scripts/parallel_multiple_rarefactions.py -> build/scripts-2.6 copying and adjusting scripts/split_otu_table_by_taxonomy.py -> build/scripts-2.6 copying and adjusting scripts/compare_categories.py -> build/scripts-2.6 copying and adjusting scripts/cluster_quality.py -> build/scripts-2.6 copying and adjusting scripts/beta_significance.py -> build/scripts-2.6 copying and adjusting scripts/parallel_pick_otus_uclust_ref.py -> build/scripts-2.6 copying and adjusting scripts/parallel_beta_diversity.py -> build/scripts-2.6 copying and adjusting scripts/summarize_taxa.py -> build/scripts-2.6 copying and adjusting scripts/transform_coordinate_matrices.py -> build/scripts-2.6 copying and adjusting scripts/denoiser_worker.py -> build/scripts-2.6 copying and adjusting scripts/filter_otus_by_sample.py -> build/scripts-2.6 copying and adjusting scripts/distance_matrix_from_mapping.py -> build/scripts-2.6 copying and adjusting scripts/make_distance_boxplots.py -> build/scripts-2.6 copying and adjusting scripts/count_seqs.py -> build/scripts-2.6 copying and adjusting scripts/trim_sff_primers.py -> build/scripts-2.6 copying and adjusting scripts/merge_mapping_files.py -> build/scripts-2.6 copying and adjusting scripts/trflp_file_to_otu_table.py -> build/scripts-2.6 copying and adjusting scripts/split_otu_table.py -> build/scripts-2.6 copying and adjusting scripts/make_bootstrapped_tree.py -> build/scripts-2.6 copying and adjusting scripts/make_rarefaction_plots.py -> build/scripts-2.6 copying and adjusting scripts/make_2d_plots.py -> build/scripts-2.6 copying and adjusting scripts/extract_seqs_by_sample_id.py -> build/scripts-2.6 copying and adjusting scripts/filter_alignment.py -> build/scripts-2.6 copying and adjusting scripts/make_distance_histograms.py -> build/scripts-2.6 copying and adjusting scripts/start_parallel_jobs_sc.py -> build/scripts-2.6 copying and adjusting scripts/assign_taxonomy.py -> build/scripts-2.6 copying and adjusting scripts/alpha_diversity.py -> build/scripts-2.6 copying and adjusting scripts/parallel_align_seqs_pynast.py -> build/scripts-2.6 copying and adjusting scripts/pick_reference_otus_through_otu_table.py -> build/scripts-2.6 copying and adjusting scripts/per_library_stats.py -> build/scripts-2.6 copying and adjusting scripts/consensus_tree.py -> build/scripts-2.6 copying and adjusting scripts/denoiser.py -> build/scripts-2.6 copying and adjusting scripts/make_otu_heatmap.py -> build/scripts-2.6 copying and adjusting scripts/parallel_pick_otus_blast.py -> build/scripts-2.6 copying and adjusting scripts/upgma_cluster.py -> build/scripts-2.6 copying and adjusting scripts/split_fasta_on_sample_ids.py -> build/scripts-2.6 copying and adjusting scripts/summarize_otu_by_cat.py -> build/scripts-2.6 copying and adjusting scripts/multiple_rarefactions_even_depth.py -> build/scripts-2.6 copying and adjusting scripts/make_fastq.py -> build/scripts-2.6 copying and adjusting scripts/make_otu_network.py -> build/scripts-2.6 copying and adjusting scripts/plot_taxa_summary.py -> build/scripts-2.6 copying and adjusting scripts/otu_category_significance.py -> build/scripts-2.6 copying and adjusting scripts/split_libraries_fastq.py -> build/scripts-2.6 copying and adjusting scripts/make_otu_table.py -> build/scripts-2.6 copying and adjusting scripts/split_libraries.py -> build/scripts-2.6 copying and adjusting scripts/filter_tree.py -> build/scripts-2.6 copying and adjusting scripts/filter_distance_matrix.py -> build/scripts-2.6 copying and adjusting scripts/quality_scores_plot.py -> build/scripts-2.6 copying and adjusting scripts/compare_distance_matrices.py -> build/scripts-2.6 copying and adjusting scripts/insert_seqs_into_tree.py -> build/scripts-2.6 copying and adjusting scripts/exclude_seqs_by_blast.py -> build/scripts-2.6 copying and adjusting scripts/filter_fasta.py -> build/scripts-2.6 copying and adjusting scripts/unweight_fasta.py -> build/scripts-2.6 copying and adjusting scripts/alpha_rarefaction.py -> build/scripts-2.6 copying and adjusting scripts/adjust_seq_orientation.py -> build/scripts-2.6 copying and adjusting scripts/poller_example.py -> build/scripts-2.6 copying and adjusting scripts/identify_missing_files.py -> build/scripts-2.6 copying and adjusting scripts/jackknifed_beta_diversity.py -> build/scripts-2.6 copying and adjusting scripts/convert_unifrac_sample_mapping_to_otu_table.py -> build/scripts-2.6 copying and adjusting scripts/submit_to_mgrast.py -> build/scripts-2.6 copying and adjusting scripts/process_iseq.py -> build/scripts-2.6 copying and adjusting scripts/add_qiime_labels.py -> build/scripts-2.6 copying and adjusting scripts/parallel_assign_taxonomy_rdp.py -> build/scripts-2.6 copying and adjusting scripts/beta_diversity.py -> build/scripts-2.6 copying and adjusting scripts/print_qiime_config.py -> build/scripts-2.6 copying and adjusting scripts/subsample_fasta.py -> build/scripts-2.6 copying and adjusting scripts/compare_3d_plots.py -> build/scripts-2.6 copying and adjusting scripts/inflate_denoiser_output.py -> build/scripts-2.6 copying and adjusting scripts/align_seqs.py -> build/scripts-2.6 copying and adjusting scripts/merge_otu_maps.py -> build/scripts-2.6 copying and adjusting scripts/filter_samples_from_otu_table.py -> build/scripts-2.6 copying scripts/ec2Clean -> build/scripts-2.6 copying scripts/ec2Dispatch -> build/scripts-2.6 changing mode of build/scripts-2.6/collate_alpha.py from 664 to 775 changing mode of build/scripts-2.6/supervised_learning.py from 664 to 775 changing mode of build/scripts-2.6/tree_compare.py from 664 to 775 changing mode of build/scripts-2.6/make_prefs_file.py from 664 to 775 changing mode of build/scripts-2.6/dissimilarity_mtx_stats.py from 664 to 775 changing mode of build/scripts-2.6/single_rarefaction.py from 664 to 775 changing mode of build/scripts-2.6/simsam.py from 664 to 775 changing mode of build/scripts-2.6/convert_fastaqual_to_fastq.py from 664 to 775 changing mode of build/scripts-2.6/truncate_fasta_qual_files.py from 664 to 775 changing mode of build/scripts-2.6/process_sff.py from 664 to 775 changing mode of build/scripts-2.6/relatedness.py from 664 to 775 changing mode of build/scripts-2.6/make_tep.py from 664 to 775 changing mode of build/scripts-2.6/multiple_rarefactions.py from 664 to 775 changing mode of build/scripts-2.6/validate_demultiplexed_fasta.py from 664 to 775 changing mode of build/scripts-2.6/parallel_blast.py from 664 to 775 changing mode of build/scripts-2.6/identify_chimeric_seqs.py from 664 to 775 changing mode of build/scripts-2.6/summarize_taxa_through_plots.py from 664 to 775 changing mode of build/scripts-2.6/denoiser_preprocess.py from 664 to 775 changing mode of build/scripts-2.6/make_3d_plots.py from 664 to 775 changing mode of build/scripts-2.6/truncate_reverse_primer.py from 664 to 775 changing mode of build/scripts-2.6/conditional_uncovered_probability.py from 664 to 775 changing mode of build/scripts-2.6/parallel_alpha_diversity.py from 664 to 775 changing mode of build/scripts-2.6/compare_alpha_diversity.py from 664 to 775 changing mode of build/scripts-2.6/check_id_map.py from 664 to 775 changing mode of build/scripts-2.6/blast_wrapper.py from 664 to 775 changing mode of build/scripts-2.6/neighbor_joining.py from 664 to 775 changing mode of build/scripts-2.6/make_phylogeny.py from 664 to 775 changing mode of build/scripts-2.6/fix_arb_fasta.py from 664 to 775 changing mode of build/scripts-2.6/pick_subsampled_reference_otus_through_otu_table.py from 664 to 775 changing mode of build/scripts-2.6/core_qiime_analyses.py from 664 to 775 changing mode of build/scripts-2.6/make_distance_comparison_plots.py from 664 to 775 changing mode of build/scripts-2.6/denoise_wrapper.py from 664 to 775 changing mode of build/scripts-2.6/pick_rep_set.py from 664 to 775 changing mode of build/scripts-2.6/categorized_dist_scatterplot.py from 664 to 775 changing mode of build/scripts-2.6/ampliconnoise.py from 664 to 775 changing mode of build/scripts-2.6/shared_phylotypes.py from 664 to 775 changing mode of build/scripts-2.6/poller.py from 664 to 775 changing mode of build/scripts-2.6/beta_diversity_through_plots.py from 664 to 775 changing mode of build/scripts-2.6/plot_rank_abundance_graph.py from 664 to 775 changing mode of build/scripts-2.6/convert_otu_table_to_unifrac_sample_mapping.py from 664 to 775 changing mode of build/scripts-2.6/start_parallel_jobs_torque.py from 664 to 775 changing mode of build/scripts-2.6/make_library_id_lists.py from 664 to 775 changing mode of build/scripts-2.6/pick_otus_through_otu_table.py from 664 to 775 changing mode of build/scripts-2.6/make_qiime_py_file.py from 664 to 775 changing mode of build/scripts-2.6/plot_semivariogram.py from 664 to 775 changing mode of build/scripts-2.6/merge_otu_tables.py from 664 to 775 changing mode of build/scripts-2.6/make_per_library_sff.py from 664 to 775 changing mode of build/scripts-2.6/clean_raxml_parsimony_tree.py from 664 to 775 changing mode of build/scripts-2.6/make_qiime_rst_file.py from 664 to 775 changing mode of build/scripts-2.6/sort_otu_table.py from 664 to 775 changing mode of build/scripts-2.6/add_taxa.py from 664 to 775 changing mode of build/scripts-2.6/start_parallel_jobs.py from 664 to 775 changing mode of build/scripts-2.6/parallel_identify_chimeric_seqs.py from 664 to 775 changing mode of build/scripts-2.6/make_otu_heatmap_html.py from 664 to 775 changing mode of build/scripts-2.6/filter_otus_from_otu_table.py from 664 to 775 changing mode of build/scripts-2.6/parallel_assign_taxonomy_blast.py from 664 to 775 changing mode of build/scripts-2.6/nmds.py from 664 to 775 changing mode of build/scripts-2.6/pick_otus.py from 664 to 775 changing mode of build/scripts-2.6/process_qseq.py from 664 to 775 changing mode of build/scripts-2.6/principal_coordinates.py from 664 to 775 changing mode of build/scripts-2.6/parallel_multiple_rarefactions.py from 664 to 775 changing mode of build/scripts-2.6/split_otu_table_by_taxonomy.py from 664 to 775 changing mode of build/scripts-2.6/compare_categories.py from 664 to 775 changing mode of build/scripts-2.6/cluster_quality.py from 664 to 775 changing mode of build/scripts-2.6/beta_significance.py from 664 to 775 changing mode of build/scripts-2.6/parallel_pick_otus_uclust_ref.py from 664 to 775 changing mode of build/scripts-2.6/parallel_beta_diversity.py from 664 to 775 changing mode of build/scripts-2.6/summarize_taxa.py from 664 to 775 changing mode of build/scripts-2.6/transform_coordinate_matrices.py from 664 to 775 changing mode of build/scripts-2.6/denoiser_worker.py from 664 to 775 changing mode of build/scripts-2.6/filter_otus_by_sample.py from 664 to 775 changing mode of build/scripts-2.6/distance_matrix_from_mapping.py from 664 to 775 changing mode of build/scripts-2.6/make_distance_boxplots.py from 664 to 775 changing mode of build/scripts-2.6/count_seqs.py from 664 to 775 changing mode of build/scripts-2.6/trim_sff_primers.py from 664 to 775 changing mode of build/scripts-2.6/merge_mapping_files.py from 664 to 775 changing mode of build/scripts-2.6/trflp_file_to_otu_table.py from 664 to 775 changing mode of build/scripts-2.6/split_otu_table.py from 664 to 775 changing mode of build/scripts-2.6/make_bootstrapped_tree.py from 664 to 775 changing mode of build/scripts-2.6/make_rarefaction_plots.py from 664 to 775 changing mode of build/scripts-2.6/make_2d_plots.py from 664 to 775 changing mode of build/scripts-2.6/extract_seqs_by_sample_id.py from 664 to 775 changing mode of build/scripts-2.6/filter_alignment.py from 664 to 775 changing mode of 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build/scripts-2.6/parallel_assign_taxonomy_rdp.py from 664 to 775 changing mode of build/scripts-2.6/beta_diversity.py from 664 to 775 changing mode of build/scripts-2.6/print_qiime_config.py from 664 to 775 changing mode of build/scripts-2.6/subsample_fasta.py from 664 to 775 changing mode of build/scripts-2.6/compare_3d_plots.py from 664 to 775 changing mode of build/scripts-2.6/inflate_denoiser_output.py from 664 to 775 changing mode of build/scripts-2.6/align_seqs.py from 664 to 775 changing mode of build/scripts-2.6/merge_otu_maps.py from 664 to 775 changing mode of build/scripts-2.6/filter_samples_from_otu_table.py from 664 to 775 make[1]: Entering directory `/«PKGBUILDDIR»/doc' sphinx-build -b html -d _build/doctrees . _build/html Making output directory... Running Sphinx v1.1.3 loading pickled environment... not yet created building [html]: targets for 173 source files that are out of date updating environment: 173 added, 0 changed, 0 removed reading sources... [ 0%] developer/coding_guidelines reading sources... [ 1%] developer/index reading sources... [ 1%] developer/reporting_and_fixing_bugs reading sources... [ 2%] documentation/biom_format reading sources... [ 2%] documentation/file_formats reading sources... [ 3%] documentation/index reading sources... [ 4%] documentation/script_index reading sources... [ 4%] documentation/table_objects reading sources... [ 5%] index reading sources... [ 5%] install/index reading sources... [ 6%] install/install reading sources... [ 6%] install/qiime_config reading sources... [ 7%] install/ubuntu_install reading sources... [ 8%] install/upgrade reading sources... [ 8%] install/virtual_box reading sources... [ 9%] install/vm_ec2 reading sources... [ 9%] scripts/add_qiime_labels reading sources... 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[100%] tutorials/working_with_aws /«PKGBUILDDIR»/doc/install/ubuntu_install.rst:22: WARNING: Literal block ends without a blank line; unexpected unindent. /«PKGBUILDDIR»/doc/tutorials/running_supervised_learning.rst:5: WARNING: Duplicate explicit target name: "link". /«PKGBUILDDIR»/doc/tutorials/usearch_quality_filter.rst:5: WARNING: Duplicate explicit target name: "otupipe". looking for now-outdated files... none found pickling environment... done /«PKGBUILDDIR»/doc/developer/index.rst:: WARNING: document isn't included in any toctree /«PKGBUILDDIR»/doc/documentation/index.rst:: WARNING: document isn't included in any toctree /«PKGBUILDDIR»/doc/install/index.rst:: WARNING: document isn't included in any toctree /«PKGBUILDDIR»/doc/scripts/index.rst:: WARNING: document isn't included in any toctree /«PKGBUILDDIR»/doc/tutorials/index.rst:: WARNING: document isn't included in any toctree checking consistency... done preparing documents... done writing output... 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[ 69%] tutorials/../images/heatmap.png copying images... [ 72%] tutorials/../images/rarecurve.png copying images... [ 75%] tutorials/../images/configure_ebs_volume_attachment.png copying images... [ 78%] tutorials/../images/stop_instance.png copying images... [ 81%] tutorials/../images/mantel_correlogram.png copying images... [ 84%] tutorials/../images/fisheyeheatmap.png copying images... [ 87%] tutorials/../images/cyberduck_drag_and_drop_input_file.png copying images... [ 90%] tutorials/../images/cyberduck_create_output_file.png copying images... [ 93%] tutorials/../images/hist.png copying images... [ 96%] tutorials/../images/boottree.png copying images... [100%] tutorials/../images/UPGMAbytreatment.png copying static files... done dumping search index... done dumping object inventory... done build succeeded, 8 warnings. Build finished. The HTML pages are in _build/html. make[1]: Leaving directory `/«PKGBUILDDIR»/doc' Local documentation built with Sphinx. Open to following path with a web browser: /«PKGBUILDDIR»/doc/_build/html/index.html make[1]: Entering directory `/«PKGBUILDDIR»/qiime/support_files/denoiser/FlowgramAlignment' ghc --make -O2 FlowgramAli_4frame Linking FlowgramAli_4frame ... clang: warning: -Wl,--hash-size=31: 'linker' input unused when '-c' is present clang: warning: -Wl,--reduce-memory-overheads: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Izh_static_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Czh_static_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Fzh_static_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Dzh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziPtr_Ptr_static_info' clang: warning: argument unused during compilation: '-u base_GHCziWord_Wzh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziInt_I8zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziInt_I16zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziInt_I32zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziInt_I64zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziWord_W8zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziWord_W16zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziWord_W32zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziWord_W64zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziStable_StablePtr_static_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Izh_con_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Czh_con_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Fzh_con_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Dzh_con_info' clang: warning: argument unused during compilation: '-u base_GHCziPtr_Ptr_con_info' clang: warning: argument unused during compilation: '-u base_GHCziPtr_FunPtr_con_info' clang: warning: argument unused during compilation: '-u base_GHCziStable_StablePtr_con_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_False_closure' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_True_closure' clang: warning: argument unused during compilation: '-u base_GHCziPack_unpackCString_closure' clang: warning: argument unused during compilation: '-u base_GHCziIOziException_stackOverflow_closure' clang: warning: argument unused during compilation: '-u base_GHCziIOziException_heapOverflow_closure' clang: warning: argument unused during compilation: '-u base_ControlziExceptionziBase_nonTermination_closure' clang: warning: argument unused during compilation: '-u base_GHCziIOziException_blockedIndefinitelyOnMVar_closure' clang: warning: argument unused during compilation: '-u base_GHCziIOziException_blockedIndefinitelyOnSTM_closure' clang: warning: argument unused during compilation: '-u base_ControlziExceptionziBase_nestedAtomically_closure' clang: warning: argument unused during compilation: '-u base_GHCziWeak_runFinalizzerBatch_closure' clang: warning: argument unused during compilation: '-u base_GHCziTopHandler_flushStdHandles_closure' clang: warning: argument unused during compilation: '-u base_GHCziTopHandler_runIO_closure' clang: warning: argument unused during compilation: '-u base_GHCziTopHandler_runNonIO_closure' clang: warning: argument unused during compilation: '-u base_GHCziConcziIO_ensureIOManagerIsRunning_closure' clang: warning: argument unused during compilation: '-u base_GHCziConcziSync_runSparks_closure' clang: warning: argument unused during compilation: '-u base_GHCziConcziSignal_runHandlers_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_exit_': (.text+0x49): undefined reference to `base_GHCziTopHandler_flushStdHandles_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x19b): undefined reference to `base_GHCziTopHandler_runIO_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1a5): undefined reference to `base_GHCziTopHandler_runNonIO_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1af): undefined reference to `base_GHCziTopHandler_flushStdHandles_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1b9): undefined reference to `base_GHCziWeak_runFinalizzerBatch_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1c3): undefined reference to `base_GHCziIOziException_stackOverflow_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1cd): undefined reference to `base_GHCziIOziException_heapOverflow_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1d7): undefined reference to `base_GHCziPack_unpackCString_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1e1): undefined reference to `base_GHCziIOziException_blockedIndefinitelyOnMVar_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1eb): undefined reference to `base_ControlziExceptionziBase_nonTermination_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1f5): undefined reference to `base_GHCziIOziException_blockedIndefinitelyOnSTM_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1ff): undefined reference to `base_ControlziExceptionziBase_nestedAtomically_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x209): undefined reference to `base_GHCziConcziSync_runSparks_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x213): undefined reference to `base_GHCziConcziIO_ensureIOManagerIsRunning_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x21d): undefined reference to `base_GHCziConcziSignal_runHandlers_closure' /usr/lib/ghc/libHSrts.a(Schedule.o): In function `scheduleWaitThread': (.text+0xed5): undefined reference to `base_ControlziExceptionziBase_nonTermination_closure' /usr/lib/ghc/libHSrts.a(Schedule.o): In function `resurrectThreads': (.text+0x1581): undefined reference to `base_ControlziExceptionziBase_nonTermination_closure' /usr/lib/ghc/libHSrts.a(Schedule.o): In function `resurrectThreads': (.text+0x15a1): undefined reference to `base_GHCziIOziException_blockedIndefinitelyOnSTM_closure' /usr/lib/ghc/libHSrts.a(Schedule.o): In function `resurrectThreads': (.text+0x15c1): undefined reference to `base_GHCziIOziException_blockedIndefinitelyOnMVar_closure' /usr/lib/ghc/libHSrts.a(Threads.o): In function `threadStackOverflow': (.text+0x6e1): undefined reference to `base_GHCziIOziException_stackOverflow_closure' /usr/lib/ghc/libHSrts.a(Weak.o): In function `scheduleFinalizers': (.text+0x1e2): undefined reference to `base_GHCziWeak_runFinalizzerBatch_closure' /usr/lib/ghc/libHSrts.a(Signals.o): In function `startSignalHandlers': (.text+0x7e2): undefined reference to `base_GHCziConcziSignal_runHandlers_closure' /usr/lib/ghc/libHSrts.a(PrimOps.o):(.text+0xfd8): undefined reference to `base_ControlziExceptionziBase_nestedAtomically_closure' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkInt16': (.text+0x72): undefined reference to `base_GHCziInt_I16zh_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkWord': (.text+0xd1): undefined reference to `base_GHCziWord_Wzh_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkWord8': (.text+0xf2): undefined reference to `base_GHCziWord_W8zh_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkWord16': (.text+0x111): undefined reference to `base_GHCziWord_W16zh_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkDouble': (.text+0x1a6): undefined reference to `ghczmprim_GHCziTypes_Dzh_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkStablePtr': (.text+0x1d1): undefined reference to `base_GHCziStable_StablePtr_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkFunPtr': (.text+0x211): undefined reference to `base_GHCziPtr_FunPtr_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkString': (.text+0x290): undefined reference to `base_GHCziPack_unpackCString_closure' clang: error: linker command failed with exit code 1 (use -v to see invocation) make[1]: *** [FlowgramAli_4frame] Error 1 make[1]: Leaving directory `/«PKGBUILDDIR»/qiime/support_files/denoiser/FlowgramAlignment' make[1]: Entering directory `/«PKGBUILDDIR»/qiime/support_files/denoiser/FlowgramAlignment' cp FlowgramAli_4frame ../bin/ cp: cannot stat `FlowgramAli_4frame': No such file or directory make[1]: *** [install] Error 1 make[1]: Leaving directory `/«PKGBUILDDIR»/qiime/support_files/denoiser/FlowgramAlignment' Denoiser built. running build running build_py creating build/lib.linux-x86_64-2.7 creating build/lib.linux-x86_64-2.7/qiime copying qiime/trim_sff_primers.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/collate_alpha.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/supervised_learning.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/tree_compare.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/simsam.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/test.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/convert_fastaqual_to_fastq.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/truncate_fasta_qual_files.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/process_sff.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/validate_demultiplexed_fasta.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/identify_chimeric_seqs.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/sort.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/make_3d_plots.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/truncate_reverse_primer.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/conditional_uncovered_probability.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/compare_alpha_diversity.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/check_id_map.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/make_phylogeny.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/pick_subsampled_reference_otus_through_otu_table.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/denoise_wrapper.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/util.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/golay.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/pick_rep_set.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/categorized_dist_scatterplot.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/shared_phylotypes.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/plot_rank_abundance_graph.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/split.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/make_library_id_lists.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/plot_semivariogram.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/make_per_library_sff.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/clean_raxml_parsimony_tree.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/make_otu_heatmap_html.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/hierarchical_cluster.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/nmds.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/pick_otus.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/principal_coordinates.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/biplots.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/quality.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/cluster_quality.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/summarize_taxa.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/colors.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/workflow.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/transform_coordinate_matrices.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/filter_otus_by_sample.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/distance_matrix_from_mapping.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/longitudinal_otu_category_significance.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/merge_mapping_files.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/make_bootstrapped_tree.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/make_rarefaction_plots.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/make_2d_plots.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/__init__.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/group.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/filter_alignment.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/make_distance_histograms.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/assign_taxonomy.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/alpha_diversity.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/filter.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/make_otu_heatmap.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/make_fastq.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/make_otu_network.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/plot_taxa_summary.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/otu_category_significance.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/split_libraries_fastq.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/make_otu_table.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/format.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/rarefaction.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/split_libraries.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/quality_scores_plot.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/compare_distance_matrices.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/insert_seqs_into_tree.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/exclude_seqs_by_blast.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/relatedness_library.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/beta_metrics.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/adjust_seq_orientation.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/submit_to_mgrast.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/add_qiime_labels.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/beta_diversity.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/hamming.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/stats.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/align_seqs.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/parse.py -> build/lib.linux-x86_64-2.7/qiime copying qiime/barcode.py -> build/lib.linux-x86_64-2.7/qiime creating build/lib.linux-x86_64-2.7/qiime/parallel copying qiime/parallel/assign_taxonomy_blast.py -> build/lib.linux-x86_64-2.7/qiime/parallel copying qiime/parallel/pick_otus_uclust_ref.py -> build/lib.linux-x86_64-2.7/qiime/parallel copying qiime/parallel/blast.py -> build/lib.linux-x86_64-2.7/qiime/parallel copying qiime/parallel/multiple_rarefactions.py -> build/lib.linux-x86_64-2.7/qiime/parallel copying qiime/parallel/identify_chimeric_seqs.py -> build/lib.linux-x86_64-2.7/qiime/parallel copying qiime/parallel/pick_otus_blast.py -> build/lib.linux-x86_64-2.7/qiime/parallel copying qiime/parallel/util.py -> build/lib.linux-x86_64-2.7/qiime/parallel copying qiime/parallel/poller.py -> build/lib.linux-x86_64-2.7/qiime/parallel copying qiime/parallel/assign_taxonomy_rdp.py -> build/lib.linux-x86_64-2.7/qiime/parallel copying qiime/parallel/__init__.py -> build/lib.linux-x86_64-2.7/qiime/parallel copying qiime/parallel/alpha_diversity.py -> build/lib.linux-x86_64-2.7/qiime/parallel copying qiime/parallel/align_seqs_pynast.py -> build/lib.linux-x86_64-2.7/qiime/parallel copying qiime/parallel/beta_diversity.py -> build/lib.linux-x86_64-2.7/qiime/parallel creating build/lib.linux-x86_64-2.7/qiime/pycogent_backports copying qiime/pycogent_backports/tree.py -> build/lib.linux-x86_64-2.7/qiime/pycogent_backports copying qiime/pycogent_backports/muscle.py -> build/lib.linux-x86_64-2.7/qiime/pycogent_backports copying qiime/pycogent_backports/raxml_v730.py -> build/lib.linux-x86_64-2.7/qiime/pycogent_backports copying qiime/pycogent_backports/rtax.py -> build/lib.linux-x86_64-2.7/qiime/pycogent_backports copying qiime/pycogent_backports/parsinsert.py -> build/lib.linux-x86_64-2.7/qiime/pycogent_backports copying qiime/pycogent_backports/uclust.py -> build/lib.linux-x86_64-2.7/qiime/pycogent_backports copying qiime/pycogent_backports/rdp_classifier.py -> build/lib.linux-x86_64-2.7/qiime/pycogent_backports copying qiime/pycogent_backports/mothur.py -> build/lib.linux-x86_64-2.7/qiime/pycogent_backports copying qiime/pycogent_backports/pplacer.py -> build/lib.linux-x86_64-2.7/qiime/pycogent_backports copying qiime/pycogent_backports/usearch.py -> build/lib.linux-x86_64-2.7/qiime/pycogent_backports copying qiime/pycogent_backports/__init__.py -> build/lib.linux-x86_64-2.7/qiime/pycogent_backports copying qiime/pycogent_backports/guppy.py -> build/lib.linux-x86_64-2.7/qiime/pycogent_backports copying qiime/pycogent_backports/distribution_plots.py -> build/lib.linux-x86_64-2.7/qiime/pycogent_backports creating build/lib.linux-x86_64-2.7/qiime/denoiser copying qiime/denoiser/utils.py -> build/lib.linux-x86_64-2.7/qiime/denoiser copying qiime/denoiser/denoise_worker.py -> build/lib.linux-x86_64-2.7/qiime/denoiser copying qiime/denoiser/denoise_postprocess.py -> build/lib.linux-x86_64-2.7/qiime/denoiser copying qiime/denoiser/flowgram_filter.py -> build/lib.linux-x86_64-2.7/qiime/denoiser copying qiime/denoiser/flowgram_clustering.py -> build/lib.linux-x86_64-2.7/qiime/denoiser copying qiime/denoiser/__init__.py -> build/lib.linux-x86_64-2.7/qiime/denoiser copying qiime/denoiser/preprocess.py -> build/lib.linux-x86_64-2.7/qiime/denoiser copying qiime/denoiser/make_cluster_jobs.py -> build/lib.linux-x86_64-2.7/qiime/denoiser copying qiime/denoiser/cluster_utils.py -> build/lib.linux-x86_64-2.7/qiime/denoiser creating build/lib.linux-x86_64-2.7/qiime/support_files copying qiime/support_files/qiime_config -> build/lib.linux-x86_64-2.7/qiime/support_files creating build/lib.linux-x86_64-2.7/qiime/support_files/css copying qiime/support_files/css/qiime_style.css -> build/lib.linux-x86_64-2.7/qiime/support_files/css creating build/lib.linux-x86_64-2.7/qiime/support_files/images copying qiime/support_files/images/qiime_header.png -> build/lib.linux-x86_64-2.7/qiime/support_files/images creating build/lib.linux-x86_64-2.7/qiime/support_files/js copying qiime/support_files/js/jquery.tablednd_0_5.js -> build/lib.linux-x86_64-2.7/qiime/support_files/js copying qiime/support_files/js/jquery.js -> build/lib.linux-x86_64-2.7/qiime/support_files/js copying qiime/support_files/js/histograms.js -> build/lib.linux-x86_64-2.7/qiime/support_files/js copying qiime/support_files/js/otu_count_display.js -> build/lib.linux-x86_64-2.7/qiime/support_files/js copying qiime/support_files/js/overlib.js -> build/lib.linux-x86_64-2.7/qiime/support_files/js creating build/lib.linux-x86_64-2.7/qiime/support_files/R copying qiime/support_files/R/loaddata.r -> build/lib.linux-x86_64-2.7/qiime/support_files/R copying qiime/support_files/R/util.r -> build/lib.linux-x86_64-2.7/qiime/support_files/R copying qiime/support_files/R/randomforests_util.r -> build/lib.linux-x86_64-2.7/qiime/support_files/R copying qiime/support_files/R/randomforests.r -> build/lib.linux-x86_64-2.7/qiime/support_files/R copying qiime/support_files/R/rda.r -> build/lib.linux-x86_64-2.7/qiime/support_files/R copying qiime/support_files/R/mrpp.r -> build/lib.linux-x86_64-2.7/qiime/support_files/R copying qiime/support_files/R/morans_i.r -> build/lib.linux-x86_64-2.7/qiime/support_files/R copying qiime/support_files/R/betadisper.r -> build/lib.linux-x86_64-2.7/qiime/support_files/R copying qiime/support_files/R/adonis.r -> build/lib.linux-x86_64-2.7/qiime/support_files/R creating build/lib.linux-x86_64-2.7/qiime/support_files/denoiser creating build/lib.linux-x86_64-2.7/qiime/support_files/denoiser/Data copying qiime/support_files/denoiser/Data/FLX_error_profile.dat -> build/lib.linux-x86_64-2.7/qiime/support_files/denoiser/Data copying qiime/support_files/denoiser/Data/Titanium_error_profile.dat -> build/lib.linux-x86_64-2.7/qiime/support_files/denoiser/Data copying qiime/support_files/denoiser/Data/probabilities.txt -> build/lib.linux-x86_64-2.7/qiime/support_files/denoiser/Data creating build/lib.linux-x86_64-2.7/qiime/support_files/denoiser/TestData copying qiime/support_files/denoiser/TestData/test_flow_file.dat -> build/lib.linux-x86_64-2.7/qiime/support_files/denoiser/TestData copying qiime/support_files/denoiser/TestData/denoiser_test_set.sff.txt -> build/lib.linux-x86_64-2.7/qiime/support_files/denoiser/TestData copying qiime/support_files/denoiser/TestData/tiny_test.sff.txt -> build/lib.linux-x86_64-2.7/qiime/support_files/denoiser/TestData copying qiime/support_files/denoiser/TestData/test_set_seqs.fna -> build/lib.linux-x86_64-2.7/qiime/support_files/denoiser/TestData running build_scripts creating build/scripts-2.7 copying and adjusting scripts/collate_alpha.py -> build/scripts-2.7 copying and adjusting scripts/supervised_learning.py -> build/scripts-2.7 copying and adjusting scripts/tree_compare.py -> build/scripts-2.7 copying and adjusting scripts/make_prefs_file.py -> build/scripts-2.7 copying and adjusting scripts/dissimilarity_mtx_stats.py -> build/scripts-2.7 copying and adjusting scripts/single_rarefaction.py -> build/scripts-2.7 copying and adjusting scripts/simsam.py -> build/scripts-2.7 copying and adjusting scripts/convert_fastaqual_to_fastq.py -> build/scripts-2.7 copying and adjusting scripts/truncate_fasta_qual_files.py -> build/scripts-2.7 copying and adjusting scripts/process_sff.py -> build/scripts-2.7 copying and adjusting scripts/relatedness.py -> build/scripts-2.7 copying and adjusting scripts/make_tep.py -> build/scripts-2.7 copying and adjusting scripts/multiple_rarefactions.py -> build/scripts-2.7 copying and adjusting scripts/validate_demultiplexed_fasta.py -> build/scripts-2.7 copying and adjusting scripts/parallel_blast.py -> build/scripts-2.7 copying and adjusting scripts/identify_chimeric_seqs.py -> build/scripts-2.7 copying and adjusting scripts/summarize_taxa_through_plots.py -> build/scripts-2.7 copying and adjusting scripts/denoiser_preprocess.py -> build/scripts-2.7 copying and adjusting scripts/make_3d_plots.py -> build/scripts-2.7 copying and adjusting scripts/truncate_reverse_primer.py -> build/scripts-2.7 copying and adjusting scripts/conditional_uncovered_probability.py -> build/scripts-2.7 copying and adjusting scripts/parallel_alpha_diversity.py -> build/scripts-2.7 copying and adjusting scripts/compare_alpha_diversity.py -> build/scripts-2.7 copying and adjusting scripts/check_id_map.py -> build/scripts-2.7 copying and adjusting scripts/blast_wrapper.py -> build/scripts-2.7 copying and adjusting scripts/neighbor_joining.py -> build/scripts-2.7 copying and adjusting scripts/make_phylogeny.py -> build/scripts-2.7 copying and adjusting scripts/fix_arb_fasta.py -> build/scripts-2.7 copying and adjusting scripts/pick_subsampled_reference_otus_through_otu_table.py -> build/scripts-2.7 copying and adjusting scripts/core_qiime_analyses.py -> build/scripts-2.7 copying and adjusting scripts/make_distance_comparison_plots.py -> build/scripts-2.7 copying and adjusting scripts/denoise_wrapper.py -> build/scripts-2.7 copying and adjusting scripts/pick_rep_set.py -> build/scripts-2.7 copying and adjusting scripts/categorized_dist_scatterplot.py -> build/scripts-2.7 copying and adjusting scripts/ampliconnoise.py -> build/scripts-2.7 copying and adjusting scripts/shared_phylotypes.py -> build/scripts-2.7 copying and adjusting scripts/poller.py -> build/scripts-2.7 copying and adjusting scripts/beta_diversity_through_plots.py -> build/scripts-2.7 copying and adjusting scripts/plot_rank_abundance_graph.py -> build/scripts-2.7 copying and adjusting scripts/convert_otu_table_to_unifrac_sample_mapping.py -> build/scripts-2.7 copying and adjusting scripts/start_parallel_jobs_torque.py -> build/scripts-2.7 copying and adjusting scripts/make_library_id_lists.py -> build/scripts-2.7 copying and adjusting scripts/pick_otus_through_otu_table.py -> build/scripts-2.7 copying and adjusting scripts/make_qiime_py_file.py -> build/scripts-2.7 copying and adjusting scripts/plot_semivariogram.py -> build/scripts-2.7 copying and adjusting scripts/merge_otu_tables.py -> build/scripts-2.7 copying and adjusting scripts/make_per_library_sff.py -> build/scripts-2.7 copying and adjusting scripts/clean_raxml_parsimony_tree.py -> build/scripts-2.7 copying and adjusting scripts/make_qiime_rst_file.py -> build/scripts-2.7 copying and adjusting scripts/sort_otu_table.py -> build/scripts-2.7 copying and adjusting scripts/add_taxa.py -> build/scripts-2.7 copying and adjusting scripts/start_parallel_jobs.py -> build/scripts-2.7 copying and adjusting scripts/parallel_identify_chimeric_seqs.py -> build/scripts-2.7 copying and adjusting scripts/make_otu_heatmap_html.py -> build/scripts-2.7 copying and adjusting scripts/filter_otus_from_otu_table.py -> build/scripts-2.7 copying and adjusting scripts/parallel_assign_taxonomy_blast.py -> build/scripts-2.7 copying and adjusting scripts/nmds.py -> build/scripts-2.7 copying and adjusting scripts/pick_otus.py -> build/scripts-2.7 copying and adjusting scripts/process_qseq.py -> build/scripts-2.7 copying and adjusting scripts/principal_coordinates.py -> build/scripts-2.7 copying and adjusting scripts/parallel_multiple_rarefactions.py -> build/scripts-2.7 copying and adjusting scripts/split_otu_table_by_taxonomy.py -> build/scripts-2.7 copying and adjusting scripts/compare_categories.py -> build/scripts-2.7 copying and adjusting scripts/cluster_quality.py -> build/scripts-2.7 copying and adjusting scripts/beta_significance.py -> build/scripts-2.7 copying and adjusting scripts/parallel_pick_otus_uclust_ref.py -> build/scripts-2.7 copying and adjusting scripts/parallel_beta_diversity.py -> build/scripts-2.7 copying and adjusting scripts/summarize_taxa.py -> build/scripts-2.7 copying and adjusting scripts/transform_coordinate_matrices.py -> build/scripts-2.7 copying and adjusting scripts/denoiser_worker.py -> build/scripts-2.7 copying and adjusting scripts/filter_otus_by_sample.py -> build/scripts-2.7 copying and adjusting scripts/distance_matrix_from_mapping.py -> build/scripts-2.7 copying and adjusting scripts/make_distance_boxplots.py -> build/scripts-2.7 copying and adjusting scripts/count_seqs.py -> build/scripts-2.7 copying and adjusting scripts/trim_sff_primers.py -> build/scripts-2.7 copying and adjusting scripts/merge_mapping_files.py -> build/scripts-2.7 copying and adjusting scripts/trflp_file_to_otu_table.py -> build/scripts-2.7 copying and adjusting scripts/split_otu_table.py -> build/scripts-2.7 copying and adjusting scripts/make_bootstrapped_tree.py -> build/scripts-2.7 copying and adjusting scripts/make_rarefaction_plots.py -> build/scripts-2.7 copying and adjusting scripts/make_2d_plots.py -> build/scripts-2.7 copying and adjusting scripts/extract_seqs_by_sample_id.py -> build/scripts-2.7 copying and adjusting scripts/filter_alignment.py -> build/scripts-2.7 copying and adjusting scripts/make_distance_histograms.py -> build/scripts-2.7 copying and adjusting scripts/start_parallel_jobs_sc.py -> build/scripts-2.7 copying and adjusting scripts/assign_taxonomy.py -> build/scripts-2.7 copying and adjusting scripts/alpha_diversity.py -> build/scripts-2.7 copying and adjusting scripts/parallel_align_seqs_pynast.py -> build/scripts-2.7 copying and adjusting scripts/pick_reference_otus_through_otu_table.py -> build/scripts-2.7 copying and adjusting scripts/per_library_stats.py -> build/scripts-2.7 copying and adjusting scripts/consensus_tree.py -> build/scripts-2.7 copying and adjusting scripts/denoiser.py -> build/scripts-2.7 copying and adjusting scripts/make_otu_heatmap.py -> build/scripts-2.7 copying and adjusting scripts/parallel_pick_otus_blast.py -> build/scripts-2.7 copying and adjusting scripts/upgma_cluster.py -> build/scripts-2.7 copying and adjusting scripts/split_fasta_on_sample_ids.py -> build/scripts-2.7 copying and adjusting scripts/summarize_otu_by_cat.py -> build/scripts-2.7 copying and adjusting scripts/multiple_rarefactions_even_depth.py -> build/scripts-2.7 copying and adjusting scripts/make_fastq.py -> build/scripts-2.7 copying and adjusting scripts/make_otu_network.py -> build/scripts-2.7 copying and adjusting scripts/plot_taxa_summary.py -> build/scripts-2.7 copying and adjusting scripts/otu_category_significance.py -> build/scripts-2.7 copying and adjusting scripts/split_libraries_fastq.py -> build/scripts-2.7 copying and adjusting scripts/make_otu_table.py -> build/scripts-2.7 copying and adjusting scripts/split_libraries.py -> build/scripts-2.7 copying and adjusting scripts/filter_tree.py -> build/scripts-2.7 copying and adjusting scripts/filter_distance_matrix.py -> build/scripts-2.7 copying and adjusting scripts/quality_scores_plot.py -> build/scripts-2.7 copying and adjusting scripts/compare_distance_matrices.py -> build/scripts-2.7 copying and adjusting scripts/insert_seqs_into_tree.py -> build/scripts-2.7 copying and adjusting scripts/exclude_seqs_by_blast.py -> build/scripts-2.7 copying and adjusting scripts/filter_fasta.py -> build/scripts-2.7 copying and adjusting scripts/unweight_fasta.py -> build/scripts-2.7 copying and adjusting scripts/alpha_rarefaction.py -> build/scripts-2.7 copying and adjusting scripts/adjust_seq_orientation.py -> build/scripts-2.7 copying and adjusting scripts/poller_example.py -> build/scripts-2.7 copying and adjusting scripts/identify_missing_files.py -> build/scripts-2.7 copying and adjusting scripts/jackknifed_beta_diversity.py -> build/scripts-2.7 copying and adjusting scripts/convert_unifrac_sample_mapping_to_otu_table.py -> build/scripts-2.7 copying and adjusting scripts/submit_to_mgrast.py -> build/scripts-2.7 copying and adjusting scripts/process_iseq.py -> build/scripts-2.7 copying and adjusting scripts/add_qiime_labels.py -> build/scripts-2.7 copying and adjusting scripts/parallel_assign_taxonomy_rdp.py -> build/scripts-2.7 copying and adjusting scripts/beta_diversity.py -> build/scripts-2.7 copying and adjusting scripts/print_qiime_config.py -> build/scripts-2.7 copying and adjusting scripts/subsample_fasta.py -> build/scripts-2.7 copying and adjusting scripts/compare_3d_plots.py -> build/scripts-2.7 copying and adjusting scripts/inflate_denoiser_output.py -> build/scripts-2.7 copying and adjusting scripts/align_seqs.py -> build/scripts-2.7 copying and adjusting scripts/merge_otu_maps.py -> build/scripts-2.7 copying and adjusting scripts/filter_samples_from_otu_table.py -> build/scripts-2.7 copying scripts/ec2Clean -> build/scripts-2.7 copying scripts/ec2Dispatch -> build/scripts-2.7 changing mode of build/scripts-2.7/collate_alpha.py from 664 to 775 changing mode of build/scripts-2.7/supervised_learning.py from 664 to 775 changing mode of build/scripts-2.7/tree_compare.py from 664 to 775 changing mode of build/scripts-2.7/make_prefs_file.py from 664 to 775 changing mode of build/scripts-2.7/dissimilarity_mtx_stats.py from 664 to 775 changing mode of build/scripts-2.7/single_rarefaction.py from 664 to 775 changing mode of build/scripts-2.7/simsam.py from 664 to 775 changing mode of build/scripts-2.7/convert_fastaqual_to_fastq.py from 664 to 775 changing mode of build/scripts-2.7/truncate_fasta_qual_files.py from 664 to 775 changing mode of build/scripts-2.7/process_sff.py from 664 to 775 changing mode of build/scripts-2.7/relatedness.py from 664 to 775 changing mode of build/scripts-2.7/make_tep.py from 664 to 775 changing mode of build/scripts-2.7/multiple_rarefactions.py from 664 to 775 changing mode of build/scripts-2.7/validate_demultiplexed_fasta.py from 664 to 775 changing mode of build/scripts-2.7/parallel_blast.py from 664 to 775 changing mode of build/scripts-2.7/identify_chimeric_seqs.py from 664 to 775 changing mode of build/scripts-2.7/summarize_taxa_through_plots.py from 664 to 775 changing mode of build/scripts-2.7/denoiser_preprocess.py from 664 to 775 changing mode of build/scripts-2.7/make_3d_plots.py from 664 to 775 changing mode of build/scripts-2.7/truncate_reverse_primer.py from 664 to 775 changing mode of build/scripts-2.7/conditional_uncovered_probability.py from 664 to 775 changing mode of build/scripts-2.7/parallel_alpha_diversity.py from 664 to 775 changing mode of build/scripts-2.7/compare_alpha_diversity.py from 664 to 775 changing mode of build/scripts-2.7/check_id_map.py from 664 to 775 changing mode of build/scripts-2.7/blast_wrapper.py from 664 to 775 changing mode of build/scripts-2.7/neighbor_joining.py from 664 to 775 changing mode of build/scripts-2.7/make_phylogeny.py from 664 to 775 changing mode of build/scripts-2.7/fix_arb_fasta.py from 664 to 775 changing mode of build/scripts-2.7/pick_subsampled_reference_otus_through_otu_table.py from 664 to 775 changing mode of build/scripts-2.7/core_qiime_analyses.py from 664 to 775 changing mode of build/scripts-2.7/make_distance_comparison_plots.py from 664 to 775 changing mode of build/scripts-2.7/denoise_wrapper.py from 664 to 775 changing mode of build/scripts-2.7/pick_rep_set.py from 664 to 775 changing mode of build/scripts-2.7/categorized_dist_scatterplot.py from 664 to 775 changing mode of build/scripts-2.7/ampliconnoise.py from 664 to 775 changing mode of build/scripts-2.7/shared_phylotypes.py from 664 to 775 changing mode of build/scripts-2.7/poller.py from 664 to 775 changing mode of build/scripts-2.7/beta_diversity_through_plots.py from 664 to 775 changing mode of build/scripts-2.7/plot_rank_abundance_graph.py from 664 to 775 changing mode of build/scripts-2.7/convert_otu_table_to_unifrac_sample_mapping.py from 664 to 775 changing mode of build/scripts-2.7/start_parallel_jobs_torque.py from 664 to 775 changing mode of build/scripts-2.7/make_library_id_lists.py from 664 to 775 changing mode of build/scripts-2.7/pick_otus_through_otu_table.py from 664 to 775 changing mode of build/scripts-2.7/make_qiime_py_file.py from 664 to 775 changing mode of build/scripts-2.7/plot_semivariogram.py from 664 to 775 changing mode of build/scripts-2.7/merge_otu_tables.py from 664 to 775 changing mode of build/scripts-2.7/make_per_library_sff.py from 664 to 775 changing mode of build/scripts-2.7/clean_raxml_parsimony_tree.py from 664 to 775 changing mode of build/scripts-2.7/make_qiime_rst_file.py from 664 to 775 changing mode of build/scripts-2.7/sort_otu_table.py from 664 to 775 changing mode of build/scripts-2.7/add_taxa.py from 664 to 775 changing mode of build/scripts-2.7/start_parallel_jobs.py from 664 to 775 changing mode of build/scripts-2.7/parallel_identify_chimeric_seqs.py from 664 to 775 changing mode of build/scripts-2.7/make_otu_heatmap_html.py from 664 to 775 changing mode of build/scripts-2.7/filter_otus_from_otu_table.py from 664 to 775 changing mode of build/scripts-2.7/parallel_assign_taxonomy_blast.py from 664 to 775 changing mode of build/scripts-2.7/nmds.py from 664 to 775 changing mode of build/scripts-2.7/pick_otus.py from 664 to 775 changing mode of build/scripts-2.7/process_qseq.py from 664 to 775 changing mode of build/scripts-2.7/principal_coordinates.py from 664 to 775 changing mode of build/scripts-2.7/parallel_multiple_rarefactions.py from 664 to 775 changing mode of build/scripts-2.7/split_otu_table_by_taxonomy.py from 664 to 775 changing mode of build/scripts-2.7/compare_categories.py from 664 to 775 changing mode of build/scripts-2.7/cluster_quality.py from 664 to 775 changing mode of build/scripts-2.7/beta_significance.py from 664 to 775 changing mode of build/scripts-2.7/parallel_pick_otus_uclust_ref.py from 664 to 775 changing mode of build/scripts-2.7/parallel_beta_diversity.py from 664 to 775 changing mode of build/scripts-2.7/summarize_taxa.py from 664 to 775 changing mode of build/scripts-2.7/transform_coordinate_matrices.py from 664 to 775 changing mode of build/scripts-2.7/denoiser_worker.py from 664 to 775 changing mode of build/scripts-2.7/filter_otus_by_sample.py from 664 to 775 changing mode of build/scripts-2.7/distance_matrix_from_mapping.py from 664 to 775 changing mode of build/scripts-2.7/make_distance_boxplots.py from 664 to 775 changing mode of build/scripts-2.7/count_seqs.py from 664 to 775 changing mode of build/scripts-2.7/trim_sff_primers.py from 664 to 775 changing mode of build/scripts-2.7/merge_mapping_files.py from 664 to 775 changing mode of build/scripts-2.7/trflp_file_to_otu_table.py from 664 to 775 changing mode of build/scripts-2.7/split_otu_table.py from 664 to 775 changing mode of build/scripts-2.7/make_bootstrapped_tree.py from 664 to 775 changing mode of build/scripts-2.7/make_rarefaction_plots.py from 664 to 775 changing mode of build/scripts-2.7/make_2d_plots.py from 664 to 775 changing mode of build/scripts-2.7/extract_seqs_by_sample_id.py from 664 to 775 changing mode of build/scripts-2.7/filter_alignment.py from 664 to 775 changing mode of build/scripts-2.7/make_distance_histograms.py from 664 to 775 changing mode of build/scripts-2.7/start_parallel_jobs_sc.py from 664 to 775 changing mode of build/scripts-2.7/assign_taxonomy.py from 664 to 775 changing mode of build/scripts-2.7/alpha_diversity.py from 664 to 775 changing mode of build/scripts-2.7/parallel_align_seqs_pynast.py from 664 to 775 changing mode of build/scripts-2.7/pick_reference_otus_through_otu_table.py from 664 to 775 changing mode of build/scripts-2.7/per_library_stats.py from 664 to 775 changing mode of build/scripts-2.7/consensus_tree.py from 664 to 775 changing mode of build/scripts-2.7/denoiser.py from 664 to 775 changing mode of build/scripts-2.7/make_otu_heatmap.py from 664 to 775 changing mode of build/scripts-2.7/parallel_pick_otus_blast.py from 664 to 775 changing mode of build/scripts-2.7/upgma_cluster.py from 664 to 775 changing mode of build/scripts-2.7/split_fasta_on_sample_ids.py from 664 to 775 changing mode of build/scripts-2.7/summarize_otu_by_cat.py from 664 to 775 changing mode of build/scripts-2.7/multiple_rarefactions_even_depth.py from 664 to 775 changing mode of build/scripts-2.7/make_fastq.py from 664 to 775 changing mode of build/scripts-2.7/make_otu_network.py from 664 to 775 changing mode of build/scripts-2.7/plot_taxa_summary.py from 664 to 775 changing mode of build/scripts-2.7/otu_category_significance.py from 664 to 775 changing mode of build/scripts-2.7/split_libraries_fastq.py from 664 to 775 changing mode of build/scripts-2.7/make_otu_table.py from 664 to 775 changing mode of build/scripts-2.7/split_libraries.py from 664 to 775 changing mode of build/scripts-2.7/filter_tree.py from 664 to 775 changing mode of build/scripts-2.7/filter_distance_matrix.py from 664 to 775 changing mode of build/scripts-2.7/quality_scores_plot.py from 664 to 775 changing mode of build/scripts-2.7/compare_distance_matrices.py from 664 to 775 changing mode of build/scripts-2.7/insert_seqs_into_tree.py from 664 to 775 changing mode of build/scripts-2.7/exclude_seqs_by_blast.py from 664 to 775 changing mode of build/scripts-2.7/filter_fasta.py from 664 to 775 changing mode of build/scripts-2.7/unweight_fasta.py from 664 to 775 changing mode of build/scripts-2.7/alpha_rarefaction.py from 664 to 775 changing mode of build/scripts-2.7/adjust_seq_orientation.py from 664 to 775 changing mode of build/scripts-2.7/poller_example.py from 664 to 775 changing mode of build/scripts-2.7/identify_missing_files.py from 664 to 775 changing mode of build/scripts-2.7/jackknifed_beta_diversity.py from 664 to 775 changing mode of build/scripts-2.7/convert_unifrac_sample_mapping_to_otu_table.py from 664 to 775 changing mode of build/scripts-2.7/submit_to_mgrast.py from 664 to 775 changing mode of build/scripts-2.7/process_iseq.py from 664 to 775 changing mode of build/scripts-2.7/add_qiime_labels.py from 664 to 775 changing mode of build/scripts-2.7/parallel_assign_taxonomy_rdp.py from 664 to 775 changing mode of build/scripts-2.7/beta_diversity.py from 664 to 775 changing mode of build/scripts-2.7/print_qiime_config.py from 664 to 775 changing mode of build/scripts-2.7/subsample_fasta.py from 664 to 775 changing mode of build/scripts-2.7/compare_3d_plots.py from 664 to 775 changing mode of build/scripts-2.7/inflate_denoiser_output.py from 664 to 775 changing mode of build/scripts-2.7/align_seqs.py from 664 to 775 changing mode of build/scripts-2.7/merge_otu_maps.py from 664 to 775 changing mode of build/scripts-2.7/filter_samples_from_otu_table.py from 664 to 775 make[1]: Entering directory `/«PKGBUILDDIR»/doc' sphinx-build -b html -d _build/doctrees . _build/html Running Sphinx v1.1.3 loading pickled environment... done building [html]: targets for 0 source files that are out of date updating environment: 0 added, 0 changed, 0 removed looking for now-outdated files... none found no targets are out of date. Build finished. The HTML pages are in _build/html. make[1]: Leaving directory `/«PKGBUILDDIR»/doc' Local documentation built with Sphinx. Open to following path with a web browser: /«PKGBUILDDIR»/doc/_build/html/index.html dh_auto_test -a fakeroot debian/rules binary-arch dh binary-arch --with python2 dh_testroot -a dh_prep -a dh_installdirs -a dh_auto_install -a make[1]: Entering directory `/«PKGBUILDDIR»/qiime/support_files/denoiser/FlowgramAlignment' ghc --make -O2 FlowgramAli_4frame Linking FlowgramAli_4frame ... clang: warning: -Wl,--hash-size=31: 'linker' input unused when '-c' is present clang: warning: -Wl,--reduce-memory-overheads: 'linker' input unused when '-c' is present clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Izh_static_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Czh_static_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Fzh_static_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Dzh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziPtr_Ptr_static_info' clang: warning: argument unused during compilation: '-u base_GHCziWord_Wzh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziInt_I8zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziInt_I16zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziInt_I32zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziInt_I64zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziWord_W8zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziWord_W16zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziWord_W32zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziWord_W64zh_static_info' clang: warning: argument unused during compilation: '-u base_GHCziStable_StablePtr_static_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Izh_con_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Czh_con_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Fzh_con_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_Dzh_con_info' clang: warning: argument unused during compilation: '-u base_GHCziPtr_Ptr_con_info' clang: warning: argument unused during compilation: '-u base_GHCziPtr_FunPtr_con_info' clang: warning: argument unused during compilation: '-u base_GHCziStable_StablePtr_con_info' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_False_closure' clang: warning: argument unused during compilation: '-u ghczmprim_GHCziTypes_True_closure' clang: warning: argument unused during compilation: '-u base_GHCziPack_unpackCString_closure' clang: warning: argument unused during compilation: '-u base_GHCziIOziException_stackOverflow_closure' clang: warning: argument unused during compilation: '-u base_GHCziIOziException_heapOverflow_closure' clang: warning: argument unused during compilation: '-u base_ControlziExceptionziBase_nonTermination_closure' clang: warning: argument unused during compilation: '-u base_GHCziIOziException_blockedIndefinitelyOnMVar_closure' clang: warning: argument unused during compilation: '-u base_GHCziIOziException_blockedIndefinitelyOnSTM_closure' clang: warning: argument unused during compilation: '-u base_ControlziExceptionziBase_nestedAtomically_closure' clang: warning: argument unused during compilation: '-u base_GHCziWeak_runFinalizzerBatch_closure' clang: warning: argument unused during compilation: '-u base_GHCziTopHandler_flushStdHandles_closure' clang: warning: argument unused during compilation: '-u base_GHCziTopHandler_runIO_closure' clang: warning: argument unused during compilation: '-u base_GHCziTopHandler_runNonIO_closure' clang: warning: argument unused during compilation: '-u base_GHCziConcziIO_ensureIOManagerIsRunning_closure' clang: warning: argument unused during compilation: '-u base_GHCziConcziSync_runSparks_closure' clang: warning: argument unused during compilation: '-u base_GHCziConcziSignal_runHandlers_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_exit_': (.text+0x49): undefined reference to `base_GHCziTopHandler_flushStdHandles_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x19b): undefined reference to `base_GHCziTopHandler_runIO_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1a5): undefined reference to `base_GHCziTopHandler_runNonIO_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1af): undefined reference to `base_GHCziTopHandler_flushStdHandles_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1b9): undefined reference to `base_GHCziWeak_runFinalizzerBatch_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1c3): undefined reference to `base_GHCziIOziException_stackOverflow_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1cd): undefined reference to `base_GHCziIOziException_heapOverflow_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1d7): undefined reference to `base_GHCziPack_unpackCString_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1e1): undefined reference to `base_GHCziIOziException_blockedIndefinitelyOnMVar_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1eb): undefined reference to `base_ControlziExceptionziBase_nonTermination_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1f5): undefined reference to `base_GHCziIOziException_blockedIndefinitelyOnSTM_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x1ff): undefined reference to `base_ControlziExceptionziBase_nestedAtomically_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x209): undefined reference to `base_GHCziConcziSync_runSparks_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x213): undefined reference to `base_GHCziConcziIO_ensureIOManagerIsRunning_closure' /usr/lib/ghc/libHSrts.a(RtsStartup.o): In function `hs_init_ghc': (.text+0x21d): undefined reference to `base_GHCziConcziSignal_runHandlers_closure' /usr/lib/ghc/libHSrts.a(Schedule.o): In function `scheduleWaitThread': (.text+0xed5): undefined reference to `base_ControlziExceptionziBase_nonTermination_closure' /usr/lib/ghc/libHSrts.a(Schedule.o): In function `resurrectThreads': (.text+0x1581): undefined reference to `base_ControlziExceptionziBase_nonTermination_closure' /usr/lib/ghc/libHSrts.a(Schedule.o): In function `resurrectThreads': (.text+0x15a1): undefined reference to `base_GHCziIOziException_blockedIndefinitelyOnSTM_closure' /usr/lib/ghc/libHSrts.a(Schedule.o): In function `resurrectThreads': (.text+0x15c1): undefined reference to `base_GHCziIOziException_blockedIndefinitelyOnMVar_closure' /usr/lib/ghc/libHSrts.a(Threads.o): In function `threadStackOverflow': (.text+0x6e1): undefined reference to `base_GHCziIOziException_stackOverflow_closure' /usr/lib/ghc/libHSrts.a(Weak.o): In function `scheduleFinalizers': (.text+0x1e2): undefined reference to `base_GHCziWeak_runFinalizzerBatch_closure' /usr/lib/ghc/libHSrts.a(Signals.o): In function `startSignalHandlers': (.text+0x7e2): undefined reference to `base_GHCziConcziSignal_runHandlers_closure' /usr/lib/ghc/libHSrts.a(PrimOps.o):(.text+0xfd8): undefined reference to `base_ControlziExceptionziBase_nestedAtomically_closure' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkInt16': (.text+0x72): undefined reference to `base_GHCziInt_I16zh_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkWord': (.text+0xd1): undefined reference to `base_GHCziWord_Wzh_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkWord8': (.text+0xf2): undefined reference to `base_GHCziWord_W8zh_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkWord16': (.text+0x111): undefined reference to `base_GHCziWord_W16zh_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkDouble': (.text+0x1a6): undefined reference to `ghczmprim_GHCziTypes_Dzh_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkStablePtr': (.text+0x1d1): undefined reference to `base_GHCziStable_StablePtr_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkFunPtr': (.text+0x211): undefined reference to `base_GHCziPtr_FunPtr_con_info' /usr/lib/ghc/libHSrts.a(RtsAPI.o): In function `rts_mkString': (.text+0x290): undefined reference to `base_GHCziPack_unpackCString_closure' clang: error: linker command failed with exit code 1 (use -v to see invocation) make[1]: *** [FlowgramAli_4frame] Error 1 make[1]: Leaving directory `/«PKGBUILDDIR»/qiime/support_files/denoiser/FlowgramAlignment' make[1]: Entering directory `/«PKGBUILDDIR»/qiime/support_files/denoiser/FlowgramAlignment' cp FlowgramAli_4frame ../bin/ cp: cannot stat `FlowgramAli_4frame': No such file or directory make[1]: *** [install] Error 1 make[1]: Leaving directory `/«PKGBUILDDIR»/qiime/support_files/denoiser/FlowgramAlignment' Denoiser built. running install running build running build_py running build_scripts running install_lib creating /«PKGBUILDDIR»/debian/tmp creating /«PKGBUILDDIR»/debian/tmp/usr creating /«PKGBUILDDIR»/debian/tmp/usr/lib creating /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6 creating /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages creating /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime creating /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/support_files creating /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/support_files/denoiser creating /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/support_files/denoiser/TestData copying build/lib.linux-x86_64-2.6/qiime/support_files/denoiser/TestData/test_set_seqs.fna -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/support_files/denoiser/TestData copying build/lib.linux-x86_64-2.6/qiime/support_files/denoiser/TestData/tiny_test.sff.txt -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/support_files/denoiser/TestData copying build/lib.linux-x86_64-2.6/qiime/support_files/denoiser/TestData/denoiser_test_set.sff.txt -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/support_files/denoiser/TestData copying build/lib.linux-x86_64-2.6/qiime/support_files/denoiser/TestData/test_flow_file.dat -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/support_files/denoiser/TestData creating /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/support_files/denoiser/Data copying build/lib.linux-x86_64-2.6/qiime/support_files/denoiser/Data/probabilities.txt -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/support_files/denoiser/Data copying build/lib.linux-x86_64-2.6/qiime/support_files/denoiser/Data/Titanium_error_profile.dat -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/support_files/denoiser/Data copying build/lib.linux-x86_64-2.6/qiime/support_files/denoiser/Data/FLX_error_profile.dat -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/support_files/denoiser/Data creating /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/support_files/R copying build/lib.linux-x86_64-2.6/qiime/support_files/R/adonis.r -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/support_files/R copying build/lib.linux-x86_64-2.6/qiime/support_files/R/betadisper.r -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/support_files/R copying build/lib.linux-x86_64-2.6/qiime/support_files/R/morans_i.r -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/support_files/R copying build/lib.linux-x86_64-2.6/qiime/support_files/R/mrpp.r -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/support_files/R copying build/lib.linux-x86_64-2.6/qiime/support_files/R/rda.r -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/support_files/R copying build/lib.linux-x86_64-2.6/qiime/support_files/R/randomforests.r -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/support_files/R copying build/lib.linux-x86_64-2.6/qiime/support_files/R/randomforests_util.r -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/support_files/R copying build/lib.linux-x86_64-2.6/qiime/support_files/R/util.r -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/support_files/R copying build/lib.linux-x86_64-2.6/qiime/support_files/R/loaddata.r -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/support_files/R creating /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/support_files/js copying build/lib.linux-x86_64-2.6/qiime/support_files/js/overlib.js -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/support_files/js copying build/lib.linux-x86_64-2.6/qiime/support_files/js/otu_count_display.js -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/support_files/js copying build/lib.linux-x86_64-2.6/qiime/support_files/js/histograms.js -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/support_files/js copying build/lib.linux-x86_64-2.6/qiime/support_files/js/jquery.js -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/support_files/js copying build/lib.linux-x86_64-2.6/qiime/support_files/js/jquery.tablednd_0_5.js -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/support_files/js creating /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/support_files/images copying build/lib.linux-x86_64-2.6/qiime/support_files/images/qiime_header.png -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/support_files/images creating /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/support_files/css copying build/lib.linux-x86_64-2.6/qiime/support_files/css/qiime_style.css -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/support_files/css copying build/lib.linux-x86_64-2.6/qiime/support_files/qiime_config -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/support_files creating /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/denoiser copying build/lib.linux-x86_64-2.6/qiime/denoiser/cluster_utils.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/denoiser copying build/lib.linux-x86_64-2.6/qiime/denoiser/make_cluster_jobs.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/denoiser copying build/lib.linux-x86_64-2.6/qiime/denoiser/preprocess.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/denoiser copying build/lib.linux-x86_64-2.6/qiime/denoiser/__init__.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/denoiser copying build/lib.linux-x86_64-2.6/qiime/denoiser/flowgram_clustering.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/denoiser copying build/lib.linux-x86_64-2.6/qiime/denoiser/flowgram_filter.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/denoiser copying build/lib.linux-x86_64-2.6/qiime/denoiser/denoise_postprocess.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/denoiser copying build/lib.linux-x86_64-2.6/qiime/denoiser/denoise_worker.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/denoiser copying build/lib.linux-x86_64-2.6/qiime/denoiser/utils.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/denoiser creating /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/pycogent_backports copying build/lib.linux-x86_64-2.6/qiime/pycogent_backports/distribution_plots.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/pycogent_backports copying build/lib.linux-x86_64-2.6/qiime/pycogent_backports/guppy.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/pycogent_backports copying build/lib.linux-x86_64-2.6/qiime/pycogent_backports/__init__.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/pycogent_backports copying build/lib.linux-x86_64-2.6/qiime/pycogent_backports/usearch.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/pycogent_backports copying build/lib.linux-x86_64-2.6/qiime/pycogent_backports/pplacer.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/pycogent_backports copying build/lib.linux-x86_64-2.6/qiime/pycogent_backports/mothur.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/pycogent_backports copying build/lib.linux-x86_64-2.6/qiime/pycogent_backports/rdp_classifier.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/pycogent_backports copying build/lib.linux-x86_64-2.6/qiime/pycogent_backports/uclust.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/pycogent_backports copying build/lib.linux-x86_64-2.6/qiime/pycogent_backports/parsinsert.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/pycogent_backports copying build/lib.linux-x86_64-2.6/qiime/pycogent_backports/rtax.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/pycogent_backports copying build/lib.linux-x86_64-2.6/qiime/pycogent_backports/raxml_v730.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/pycogent_backports copying build/lib.linux-x86_64-2.6/qiime/pycogent_backports/muscle.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/pycogent_backports copying build/lib.linux-x86_64-2.6/qiime/pycogent_backports/tree.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/pycogent_backports creating /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/parallel copying build/lib.linux-x86_64-2.6/qiime/parallel/beta_diversity.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/parallel copying build/lib.linux-x86_64-2.6/qiime/parallel/align_seqs_pynast.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/parallel copying build/lib.linux-x86_64-2.6/qiime/parallel/alpha_diversity.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/parallel copying build/lib.linux-x86_64-2.6/qiime/parallel/__init__.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/parallel copying build/lib.linux-x86_64-2.6/qiime/parallel/assign_taxonomy_rdp.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/parallel copying build/lib.linux-x86_64-2.6/qiime/parallel/poller.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/parallel copying build/lib.linux-x86_64-2.6/qiime/parallel/util.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/parallel copying build/lib.linux-x86_64-2.6/qiime/parallel/pick_otus_blast.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/parallel copying build/lib.linux-x86_64-2.6/qiime/parallel/identify_chimeric_seqs.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/parallel copying build/lib.linux-x86_64-2.6/qiime/parallel/multiple_rarefactions.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/parallel copying build/lib.linux-x86_64-2.6/qiime/parallel/blast.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/parallel copying build/lib.linux-x86_64-2.6/qiime/parallel/pick_otus_uclust_ref.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/parallel copying build/lib.linux-x86_64-2.6/qiime/parallel/assign_taxonomy_blast.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime/parallel copying build/lib.linux-x86_64-2.6/qiime/barcode.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/parse.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/align_seqs.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/stats.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/hamming.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/beta_diversity.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/add_qiime_labels.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/submit_to_mgrast.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/adjust_seq_orientation.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/beta_metrics.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/relatedness_library.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/exclude_seqs_by_blast.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/insert_seqs_into_tree.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/compare_distance_matrices.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/quality_scores_plot.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/split_libraries.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/rarefaction.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/format.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/make_otu_table.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/split_libraries_fastq.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/otu_category_significance.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/plot_taxa_summary.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/make_otu_network.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/make_fastq.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/make_otu_heatmap.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/filter.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/alpha_diversity.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/assign_taxonomy.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/make_distance_histograms.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/filter_alignment.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/group.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/__init__.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/make_2d_plots.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/make_rarefaction_plots.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/make_bootstrapped_tree.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/merge_mapping_files.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/longitudinal_otu_category_significance.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/distance_matrix_from_mapping.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/filter_otus_by_sample.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/transform_coordinate_matrices.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/workflow.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/colors.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/summarize_taxa.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/cluster_quality.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/quality.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/biplots.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/principal_coordinates.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/pick_otus.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/nmds.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/hierarchical_cluster.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/make_otu_heatmap_html.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/clean_raxml_parsimony_tree.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/make_per_library_sff.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/plot_semivariogram.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/make_library_id_lists.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/split.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/plot_rank_abundance_graph.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/shared_phylotypes.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/categorized_dist_scatterplot.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/pick_rep_set.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/golay.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/util.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/denoise_wrapper.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/pick_subsampled_reference_otus_through_otu_table.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/make_phylogeny.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/check_id_map.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/compare_alpha_diversity.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/conditional_uncovered_probability.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/truncate_reverse_primer.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/make_3d_plots.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/sort.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/identify_chimeric_seqs.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/validate_demultiplexed_fasta.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/process_sff.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/truncate_fasta_qual_files.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/convert_fastaqual_to_fastq.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/test.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/simsam.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/tree_compare.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/supervised_learning.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/collate_alpha.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime copying build/lib.linux-x86_64-2.6/qiime/trim_sff_primers.py -> /«PKGBUILDDIR»/debian/tmp/usr/lib/python2.6/dist-packages/qiime running install_scripts creating /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/ec2Dispatch -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/ec2Clean -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/filter_samples_from_otu_table.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/merge_otu_maps.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/align_seqs.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/inflate_denoiser_output.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/compare_3d_plots.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/subsample_fasta.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/print_qiime_config.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/beta_diversity.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/parallel_assign_taxonomy_rdp.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/add_qiime_labels.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/process_iseq.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/submit_to_mgrast.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/convert_unifrac_sample_mapping_to_otu_table.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/jackknifed_beta_diversity.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/identify_missing_files.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/poller_example.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/adjust_seq_orientation.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/alpha_rarefaction.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/unweight_fasta.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/filter_fasta.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/exclude_seqs_by_blast.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/insert_seqs_into_tree.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/compare_distance_matrices.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/quality_scores_plot.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/filter_distance_matrix.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/filter_tree.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/split_libraries.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/make_otu_table.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/split_libraries_fastq.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/otu_category_significance.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/plot_taxa_summary.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/make_otu_network.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/make_fastq.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/multiple_rarefactions_even_depth.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/summarize_otu_by_cat.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/split_fasta_on_sample_ids.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/upgma_cluster.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/parallel_pick_otus_blast.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/make_otu_heatmap.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/denoiser.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/consensus_tree.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/per_library_stats.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/pick_reference_otus_through_otu_table.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/parallel_align_seqs_pynast.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/alpha_diversity.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/assign_taxonomy.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/start_parallel_jobs_sc.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/make_distance_histograms.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/filter_alignment.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/extract_seqs_by_sample_id.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/make_2d_plots.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/make_rarefaction_plots.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/make_bootstrapped_tree.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/split_otu_table.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/trflp_file_to_otu_table.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/merge_mapping_files.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/trim_sff_primers.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/count_seqs.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/make_distance_boxplots.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/distance_matrix_from_mapping.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/filter_otus_by_sample.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/denoiser_worker.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/transform_coordinate_matrices.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/summarize_taxa.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/parallel_beta_diversity.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/parallel_pick_otus_uclust_ref.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/beta_significance.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/cluster_quality.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/compare_categories.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/split_otu_table_by_taxonomy.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/parallel_multiple_rarefactions.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/principal_coordinates.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/process_qseq.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/pick_otus.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/nmds.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/parallel_assign_taxonomy_blast.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/filter_otus_from_otu_table.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/make_otu_heatmap_html.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/parallel_identify_chimeric_seqs.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/start_parallel_jobs.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/add_taxa.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/sort_otu_table.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/make_qiime_rst_file.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/clean_raxml_parsimony_tree.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/make_per_library_sff.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/merge_otu_tables.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/plot_semivariogram.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/make_qiime_py_file.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/pick_otus_through_otu_table.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/make_library_id_lists.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/start_parallel_jobs_torque.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/convert_otu_table_to_unifrac_sample_mapping.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/plot_rank_abundance_graph.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/beta_diversity_through_plots.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/poller.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/shared_phylotypes.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/ampliconnoise.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/categorized_dist_scatterplot.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/pick_rep_set.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/denoise_wrapper.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/make_distance_comparison_plots.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/core_qiime_analyses.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/pick_subsampled_reference_otus_through_otu_table.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/fix_arb_fasta.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/make_phylogeny.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/neighbor_joining.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/blast_wrapper.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/check_id_map.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/compare_alpha_diversity.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/parallel_alpha_diversity.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/conditional_uncovered_probability.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/truncate_reverse_primer.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/make_3d_plots.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/denoiser_preprocess.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/summarize_taxa_through_plots.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/identify_chimeric_seqs.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/parallel_blast.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/validate_demultiplexed_fasta.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/multiple_rarefactions.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/make_tep.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/relatedness.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/process_sff.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/truncate_fasta_qual_files.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/convert_fastaqual_to_fastq.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/simsam.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/single_rarefaction.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/dissimilarity_mtx_stats.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/make_prefs_file.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/tree_compare.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/supervised_learning.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin copying build/scripts-2.6/collate_alpha.py -> /«PKGBUILDDIR»/debian/tmp/usr/bin changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/ec2Dispatch to 755 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/ec2Clean to 755 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/filter_samples_from_otu_table.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/merge_otu_maps.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/align_seqs.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/inflate_denoiser_output.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/compare_3d_plots.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/subsample_fasta.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/print_qiime_config.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/beta_diversity.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/parallel_assign_taxonomy_rdp.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/add_qiime_labels.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/process_iseq.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/submit_to_mgrast.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/convert_unifrac_sample_mapping_to_otu_table.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/jackknifed_beta_diversity.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/identify_missing_files.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/poller_example.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/adjust_seq_orientation.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/alpha_rarefaction.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/unweight_fasta.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/filter_fasta.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/exclude_seqs_by_blast.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/insert_seqs_into_tree.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/compare_distance_matrices.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/quality_scores_plot.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/filter_distance_matrix.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/filter_tree.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/split_libraries.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/make_otu_table.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/split_libraries_fastq.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/otu_category_significance.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/plot_taxa_summary.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/make_otu_network.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/make_fastq.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/multiple_rarefactions_even_depth.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/summarize_otu_by_cat.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/split_fasta_on_sample_ids.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/upgma_cluster.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/parallel_pick_otus_blast.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/make_otu_heatmap.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/denoiser.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/consensus_tree.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/per_library_stats.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/pick_reference_otus_through_otu_table.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/parallel_align_seqs_pynast.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/alpha_diversity.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/assign_taxonomy.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/start_parallel_jobs_sc.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/make_distance_histograms.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/filter_alignment.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/extract_seqs_by_sample_id.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/make_2d_plots.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/make_rarefaction_plots.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/make_bootstrapped_tree.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/split_otu_table.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/trflp_file_to_otu_table.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/merge_mapping_files.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/trim_sff_primers.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/count_seqs.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/make_distance_boxplots.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/distance_matrix_from_mapping.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/filter_otus_by_sample.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/denoiser_worker.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/transform_coordinate_matrices.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/summarize_taxa.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/parallel_beta_diversity.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/parallel_pick_otus_uclust_ref.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/beta_significance.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/cluster_quality.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/compare_categories.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/split_otu_table_by_taxonomy.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/parallel_multiple_rarefactions.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/principal_coordinates.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/process_qseq.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/pick_otus.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/nmds.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/parallel_assign_taxonomy_blast.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/filter_otus_from_otu_table.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/make_otu_heatmap_html.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/parallel_identify_chimeric_seqs.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/start_parallel_jobs.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/add_taxa.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/sort_otu_table.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/make_qiime_rst_file.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/clean_raxml_parsimony_tree.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/make_per_library_sff.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/merge_otu_tables.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/plot_semivariogram.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/make_qiime_py_file.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/pick_otus_through_otu_table.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/make_library_id_lists.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/start_parallel_jobs_torque.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/convert_otu_table_to_unifrac_sample_mapping.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/plot_rank_abundance_graph.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/beta_diversity_through_plots.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/poller.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/shared_phylotypes.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/ampliconnoise.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/categorized_dist_scatterplot.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/pick_rep_set.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/denoise_wrapper.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/make_distance_comparison_plots.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/core_qiime_analyses.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/pick_subsampled_reference_otus_through_otu_table.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/fix_arb_fasta.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/make_phylogeny.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/neighbor_joining.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/blast_wrapper.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/check_id_map.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/compare_alpha_diversity.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/parallel_alpha_diversity.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/conditional_uncovered_probability.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/truncate_reverse_primer.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/make_3d_plots.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/denoiser_preprocess.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/summarize_taxa_through_plots.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/identify_chimeric_seqs.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/parallel_blast.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/validate_demultiplexed_fasta.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/multiple_rarefactions.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/make_tep.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/relatedness.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/process_sff.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/truncate_fasta_qual_files.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/convert_fastaqual_to_fastq.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/simsam.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/single_rarefaction.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/dissimilarity_mtx_stats.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/make_prefs_file.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/tree_compare.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/supervised_learning.py to 775 changing mode of /«PKGBUILDDIR»/debian/tmp/usr/bin/collate_alpha.py to 775 running install_data creating /«PKGBUILDDIR»/debian/tmp/usr/qiime creating /«PKGBUILDDIR»/debian/tmp/usr/qiime/support_files creating /«PKGBUILDDIR»/debian/tmp/usr/qiime/support_files/denoiser creating /«PKGBUILDDIR»/debian/tmp/usr/qiime/support_files/denoiser/bin error: can't copy 'qiime/support_files/denoiser/bin/FlowgramAli_4frame': doesn't exist or not a regular file dh_auto_install: python2.6 setup.py install --force --root=/«PKGBUILDDIR»/debian/tmp --no-compile -O0 --install-layout=deb returned exit code 1 make: *** [binary-arch] Error 1 dpkg-buildpackage: error: fakeroot debian/rules binary-arch gave error exit status 2 ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120623-1619 Finished ──────── E: Build failure (dpkg-buildpackage died) ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Not cleaning session: cloned chroot in use ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: amd64 Build-Space: 63252 Build-Time: 46 Distribution: unstable Fail-Stage: build Install-Time: 48 Job: qiime_1.5.0-1 Package: qiime Package-Time: 118 Source-Version: 1.5.0-1 Space: 63252 Status: attempted Version: 1.5.0-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120623-1619 Build needed 00:01:58, 63252k disc space DC-Status: Failed 119.005595s DC-Time-Estimation: 119.005595 versus expected 337 (r/m: 1.83179963093332 ; m: 119.005595)