sbuild (Debian sbuild) 0.62.6 (07 Dec 2011) on build03.raspbian.lan ╔══════════════════════════════════════════════════════════════════════════════╗ ║ mafft 6.864-1 (armhf) 01 Jun 2012 11:55 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: mafft Version: 6.864-1 Source Version: 6.864-1 Distribution: testing Architecture: armhf I: NOTICE: Log filtering will replace 'build/mafft-jWVARm/mafft-6.864' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/mafft-jWVARm' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/testing-armhf-sbuild-63ef3e2c-a73d-4e71-b9b7-13913af82002' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Get:1 http://repo.raspbian.lan testing InRelease [3588 B] Get:2 http://repo.raspbian.lan testing/main Sources [5995 kB] Get:3 http://repo.raspbian.lan testing/main armhf Packages [6841 kB] Ign http://repo.raspbian.lan testing/main Translation-en Fetched 12.8 MB in 40s (321 kB/s) Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'mafft' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/debian-med/trunk/packages/mafft/trunk/ Need to get 392 kB of source archives. Get:1 http://repo.raspbian.lan/raspbian/ testing/main mafft 6.864-1 (dsc) [1993 B] Get:2 http://repo.raspbian.lan/raspbian/ testing/main mafft 6.864-1 (tar) [384 kB] Get:3 http://repo.raspbian.lan/raspbian/ testing/main mafft 6.864-1 (diff) [5144 B] Fetched 392 kB in 0s (2456 kB/s) Download complete and in download only mode Check arch ────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-wAoZK9/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 8 not upgraded. Need to get 0 B/704 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 ... 10648 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: libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), quilt (>= 0.47) Filtered Build-Depends: libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), quilt (>= 0.47) dpkg-deb: building package `sbuild-build-depends-mafft-dummy' in `/«BUILDDIR»/resolver-JrBqwq/apt_archive/sbuild-build-depends-mafft-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install mafft 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 diffstat file gettext gettext-base groff-base html2text intltool-debian libcroco3 libffi5 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt Suggested packages: wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser libmail-box-perl procmail graphviz default-mta mail-transport-agent Recommended packages: curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils debhelper diffstat file gettext gettext-base groff-base html2text intltool-debian libcroco3 libffi5 libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db po-debconf quilt sbuild-build-depends-mafft-dummy debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 21 newly installed, 0 to remove and 8 not upgraded. Need to get 0 B/9782 kB of archives. After this operation, 25.1 MB of additional disk space will be used. Selecting previously unselected package libpcre3:armhf. (Reading database ... 10648 files and directories currently installed.) Unpacking libpcre3:armhf (from .../libpcre3_1%3a8.30-5_armhf.deb) ... Selecting previously unselected package libpipeline1:armhf. Unpacking libpipeline1:armhf (from .../libpipeline1_1.2.1-1_armhf.deb) ... Selecting previously unselected package libmagic1:armhf. Unpacking libmagic1:armhf (from .../libmagic1_5.11-1_armhf.deb) ... Selecting previously unselected package libxml2:armhf. Unpacking libxml2:armhf (from .../libxml2_2.7.8.dfsg-9.1_armhf.deb) ... Selecting previously unselected package libffi5:armhf. Unpacking libffi5:armhf (from .../libffi5_3.0.10-3+b3_armhf.deb) ... Selecting previously unselected package libglib2.0-0:armhf. Unpacking libglib2.0-0:armhf (from .../libglib2.0-0_2.32.3-1_armhf.deb) ... Selecting previously unselected package libcroco3:armhf. Unpacking libcroco3:armhf (from .../libcroco3_0.6.5-1_armhf.deb) ... Selecting previously unselected package libunistring0:armhf. Unpacking libunistring0:armhf (from .../libunistring0_0.9.3-5_armhf.deb) ... Selecting previously unselected package bsdmainutils. Unpacking bsdmainutils (from .../bsdmainutils_9.0.2_armhf.deb) ... Selecting previously unselected package groff-base. Unpacking groff-base (from .../groff-base_1.21-7_armhf.deb) ... Selecting previously unselected package man-db. Unpacking man-db (from .../man-db_2.6.1-2_armhf.deb) ... Selecting previously unselected package file. Unpacking file (from .../archives/file_5.11-1_armhf.deb) ... Selecting previously unselected package gettext-base. Unpacking gettext-base (from .../gettext-base_0.18.1.1-5+rpi1_armhf.deb) ... Selecting previously unselected package html2text. Unpacking html2text (from .../html2text_1.3.2a-15_armhf.deb) ... Selecting previously unselected package gettext. Unpacking gettext (from .../gettext_0.18.1.1-5+rpi1_armhf.deb) ... Selecting previously unselected package intltool-debian. Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ... Selecting previously unselected package po-debconf. Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ... Selecting previously unselected package debhelper. Unpacking debhelper (from .../debhelper_9.20120419_all.deb) ... Selecting previously unselected package diffstat. Unpacking diffstat (from .../diffstat_1.55-2_armhf.deb) ... Selecting previously unselected package quilt. Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ... Selecting previously unselected package sbuild-build-depends-mafft-dummy. Unpacking sbuild-build-depends-mafft-dummy (from .../sbuild-build-depends-mafft-dummy.deb) ... Setting up libpcre3:armhf (1:8.30-5) ... Setting up libpipeline1:armhf (1.2.1-1) ... Setting up libmagic1:armhf (5.11-1) ... Setting up libxml2:armhf (2.7.8.dfsg-9.1) ... Setting up libffi5:armhf (3.0.10-3+b3) ... Setting up libglib2.0-0:armhf (2.32.3-1) ... No schema files found: doing nothing. Setting up libcroco3:armhf (0.6.5-1) ... Setting up libunistring0:armhf (0.9.3-5) ... Setting up bsdmainutils (9.0.2) ... 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 (1.21-7) ... Setting up man-db (2.6.1-2) ... Building database of manual pages ... Setting up file (5.11-1) ... Setting up gettext-base (0.18.1.1-5+rpi1) ... Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-5+rpi1) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20120419) ... Setting up diffstat (1.55-2) ... Setting up quilt (0.60-2) ... Setting up sbuild-build-depends-mafft-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.2.0-2-mx5 armhf (armv7l) Toolchain package versions: binutils_2.22-6 dpkg-dev_1.16.3 g++-4.6_4.6.3-1.1+rpi2 gcc-4.6_4.6.3-1.1+rpi2 libc6-dev_2.13-32 libstdc++6_4.7.0-1.1+rpi libstdc++6-4.6-dev_4.6.3-1.1+rpi2 linux-libc-dev_3.2.12-1 Package versions: apt_0.9.3 base-files_6.7 base-passwd_3.5.24 bash_4.2-2 binutils_2.22-6 bsdmainutils_9.0.2 bsdutils_1:2.20.1-4 build-essential_11.5+b1 bzip2_1.0.6-1 coreutils_8.13-3.2 cpp_4:4.6.2-4 cpp-4.6_4.6.3-1.1+rpi2 dash_0.5.7-3 debconf_1.5.43 debfoster_2.7-1.1 debhelper_9.20120419 debian-archive-keyring_2012.3 debianutils_4.3 diffstat_1.55-2 diffutils_1:3.2-6 dpkg_1.16.3 dpkg-dev_1.16.3 e2fslibs_1.42.2-2 e2fsprogs_1.42.2-2 fakeroot_1.18.3-1 file_5.11-1 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.3-1.1+rpi2 gcc_4:4.6.2-4 gcc-4.4-base_4.4.7-1.1+rpi1 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6_4.6.3-1.1+rpi2 gcc-4.6-base_4.6.3-1.1+rpi2 gcc-4.7-base_4.7.0-1.1+rpi gettext_0.18.1.1-5+rpi1 gettext-base_0.18.1.1-5+rpi1 gnupg_1.4.12-4 gpgv_1.4.12-4 grep_2.12-2 groff-base_1.21-7 gzip_1.4-5 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-22.1 insserv_1.14.0-3 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-7 libapt-pkg4.12_0.9.3+rpi1 libattr1_1:2.4.46-7 libblkid1_2.20.1-4 libbz2-1.0_1.0.6-1 libc-bin_2.13-32 libc-dev-bin_2.13-32 libc6_2.13-32 libc6-dev_2.13-32 libclass-isa-perl_0.36-3 libcomerr2_1.42.2-2 libcroco3_0.6.5-1 libdb5.1_5.1.29-1 libdpkg-perl_1.16.3 libffi5_3.0.10-3+b3 libfile-fcntllock-perl_0.14-1 libgc1c2_1:7.1-8 libgcc1_1:4.7.0-1.1+rpi libgdbm3_1.8.3-10 libglib2.0-0_2.32.3-1 libgmp10_2:5.0.5+dfsg-1.1 libgomp1_4.7.0-1.1+rpi liblocale-gettext-perl_1.05-7 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.11-1 libmount1_2.20.1-4 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-7 libncursesw5_5.9-7 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 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libreadline6_6.2-8 libselinux1_2.1.9-2 libsemanage-common_2.1.6-2 libsemanage1_2.1.6-2 libsepol1_2.1.4-3 libslang2_2.2.4-10 libss2_1.42.2-2 libstdc++6_4.7.0-1.1+rpi libstdc++6-4.6-dev_4.6.3-1.1+rpi2 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-7 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libustr-1.0-1_1.0.4-2 libuuid1_2.20.1-4 libxml2_2.7.8.dfsg-9.1 linux-libc-dev_3.2.12-1 login_1:4.1.5-1 lsb-base_4.1+Debian4 make_3.81-8.2 man-db_2.6.1-2 mawk_1.3.3-17 mount_2.20.1-4 multiarch-support_2.13-32 ncurses-base_5.9-7 ncurses-bin_5.9-7 passwd_1:4.1.5-1 patch_2.6.1-3 perl_5.14.2-11 perl-base_5.14.2-11 perl-modules_5.14.2-11 po-debconf_1.0.16+nmu2 quilt_0.60-2 readline-common_6.2-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-mafft-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.7 sysv-rc_2.88dsf-22.1 sysvinit_2.88dsf-22.1 sysvinit-utils_2.88dsf-22.1 tar_1.26-4 tzdata_2012c-1 ucf_3.0025+nmu3 util-linux_2.20.1-4 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.7.dfsg-1 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Thu Jan 12 10:12:45 2012 UTC using RSA key ID 2295D502 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./mafft_6.864-1.dsc dpkg-source: info: extracting mafft in mafft-6.864 dpkg-source: info: unpacking mafft_6.864.orig.tar.gz dpkg-source: info: unpacking mafft_6.864-1.debian.tar.gz Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── HOME=/sbuild-nonexistent LOGNAME=buildd PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/X11R6/bin:/usr/games SCHROOT_CHROOT_NAME=testing-armhf-sbuild SCHROOT_COMMAND=env SCHROOT_GID=108 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=testing-armhf-sbuild-63ef3e2c-a73d-4e71-b9b7-13913af82002 SCHROOT_UID=106 SCHROOT_USER=buildd SHELL=/bin/sh TERM=xterm USER=buildd dpkg-buildpackage ───────────────── dpkg-buildpackage: source package mafft dpkg-buildpackage: source version 6.864-1 dpkg-source --before-build mafft-6.864 dpkg-buildpackage: host architecture armhf fakeroot debian/rules clean dh clean --with quilt dh_testdir dh_auto_clean dh_quilt_unpatch No patch removed debian/rules override_dh_clean make[1]: Entering directory `/«PKGBUILDDIR»' [ ! -f core/Makefile ] || /usr/bin/make -C core clean make[2]: Entering directory `/«PKGBUILDDIR»/core' rm -f *.o *.a *.exe *~ dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign pair2hat3s multi2hat3s rnatest pairash splittbfast disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre dndpre2 setcore replaceu restoreu version mafft mafft-homologs.rb make[2]: Leaving directory `/«PKGBUILDDIR»/core' rm -rf binaries/* scripts/* dh_clean make[1]: Leaving directory `/«PKGBUILDDIR»' debian/rules build-arch dh build-arch --with quilt dh_testdir -a dh_quilt_patch -a No series file found dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory `/«PKGBUILDDIR»' /usr/bin/make -C core PREFIX=/usr/lib/mafft ENABLE_MULTITHREAD=-Denablemultithread LIBDIR=/usr/lib/mafft/lib/mafft make[2]: Entering directory `/«PKGBUILDDIR»/core' gcc -Denablemultithread -O3 -c mtxutl.c gcc -Denablemultithread -O3 -c io.c gcc -Denablemultithread -O3 -c mltaln9.c gcc -Denablemultithread -O3 -c tddis.c gcc -Denablemultithread -O3 -c constants.c gcc -Denablemultithread -O3 -c nj.c gcc -Denablemultithread -O3 -c partQalignmm.c gcc -Denablemultithread -O3 -c partSalignmm.c gcc -Denablemultithread -O3 -c Lalignmm.c gcc -Denablemultithread -O3 -c rna.c gcc -Denablemultithread -O3 -c Salignmm.c gcc -Denablemultithread -O3 -c Ralignmm.c gcc -Denablemultithread -O3 -c Qalignmm.c gcc -Denablemultithread -O3 -c Halignmm.c gcc -Denablemultithread -O3 -c Falign.c gcc -Denablemultithread -O3 -c Falign_localhom.c gcc -Denablemultithread -O3 -c Galign11.c gcc -Denablemultithread -O3 -c MSalignmm.c gcc -Denablemultithread -O3 -c fftFunctions.c gcc -Denablemultithread -O3 -c fft.c gcc -Denablemultithread -O3 -c tditeration.c gcc -Denablemultithread -O3 -c dvtditr.c gcc -Denablemultithread -O3 -c defs.c gcc -Denablemultithread -O3 -c SAalignmm.c -o SAalignmm.o gcc -Denablemultithread -O3 -c treeOperation.c gcc -o dvtditr mtxutl.o io.o mltaln9.o tddis.o constants.o nj.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o Falign.o Falign_localhom.o Galign11.o MSalignmm.o fftFunctions.o fft.o tditeration.o dvtditr.o defs.o SAalignmm.o treeOperation.o -Denablemultithread -O3 -lm -lpthread gcc -Denablemultithread -O3 -c dndfast7.c gcc -o dndfast7 dndfast7.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o -Denablemultithread -O3 -lm -lpthread gcc -Denablemultithread -O3 -c dndblast.c gcc -o dndblast dndblast.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o -Denablemultithread -O3 -lm -lpthread gcc -Denablemultithread -O3 -c sextet5.c gcc -o sextet5 io.o constants.o mtxutl.o mltaln9.o tddis.o sextet5.o defs.o -Denablemultithread -O3 -lm -lpthread gcc -Denablemultithread -O3 -c mafft-distance.c gcc -o mafft-distance io.o constants.o mtxutl.o mltaln9.o tddis.o mafft-distance.o defs.o -Denablemultithread -O3 -lm -lpthread gcc -Denablemultithread -O3 -c MSalign11.c gcc -Denablemultithread -O3 -c suboptalign11.c gcc -Denablemultithread -O3 -c genGalign11.c gcc -Denablemultithread -O3 -c genalign11.c gcc -Denablemultithread -O3 -c Lalign11.c gcc -Denablemultithread -O3 -c pairlocalalign.c gcc -o pairlocalalign mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o Falign.o MSalignmm.o Galign11.o MSalign11.o suboptalign11.o genGalign11.o genalign11.o Lalign11.o SAalignmm.o pairlocalalign.o defs.o fft.o fftFunctions.o -Denablemultithread -O3 -lm -lpthread gcc -Denablemultithread -O3 -c pair2hat3s.c gcc -o pair2hat3s mtxutl.o io.o mltaln9.o tddis.o constants.o pair2hat3s.o defs.o fft.o fftFunctions.o -Denablemultithread -O3 -lm -lpthread gcc -Denablemultithread -O3 -c multi2hat3s.c gcc -o multi2hat3s mtxutl.o io.o mltaln9.o tddis.o constants.o multi2hat3s.o defs.o fft.o fftFunctions.o -Denablemultithread -O3 -lm -lpthread gcc -Denablemultithread -O3 -c rnatest.c gcc -o rnatest mtxutl.o io.o mltaln9.o tddis.o constants.o Lalignmm.o rna.o rnatest.o defs.o fft.o fftFunctions.o -Denablemultithread -O3 -lm -lpthread gcc -Denablemultithread -O3 -c pairash.c gcc -o pairash mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o Falign.o MSalignmm.o Galign11.o MSalign11.o suboptalign11.o genGalign11.o genalign11.o Lalign11.o SAalignmm.o pairash.o defs.o fft.o fftFunctions.o -Denablemultithread -O3 -lm -lpthread gcc -Denablemultithread -O3 -c splittbfast.c gcc -o splittbfast mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o Lalign11.o splittbfast.o defs.o fft.o fftFunctions.o -Denablemultithread -O3 -lm -lpthread gcc -Denablemultithread -O3 -c disttbfast.c gcc -Denablemultithread -O3 -c addfunctions.c gcc -o disttbfast mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o disttbfast.o defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -O3 -lm -lpthread gcc -Denablemultithread -O3 -c tbfast.c gcc -o tbfast mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o Falign.o Falign_localhom.o Galign11.o SAalignmm.o tbfast.o defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -O3 -lm -lpthread gcc -Denablemultithread -O3 -c mafft-profile.c gcc -o mafft-profile io.o mtxutl.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o MSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o SAalignmm.o Galign11.o Falign.o Falign_localhom.o fftFunctions.o fft.o mafft-profile.o defs.o -Denablemultithread -O3 -lm -lpthread gcc -Denablemultithread -O3 -c f2cl.c gcc -o f2cl mtxutl.o io.o f2cl.o constants.o defs.o -Denablemultithread -O3 -lm -lpthread gcc -Denablemultithread -O3 -c mccaskillwrap.c gcc -o mccaskillwrap mtxutl.o io.o mccaskillwrap.o constants.o defs.o mltaln9.o -Denablemultithread -O3 -lm -lpthread gcc -Denablemultithread -O3 -c contrafoldwrap.c gcc -o contrafoldwrap mtxutl.o io.o contrafoldwrap.o constants.o defs.o mltaln9.o -Denablemultithread -O3 -lm -lpthread gcc -Denablemultithread -O3 -c countlen.c gcc -o countlen mtxutl.o io.o countlen.o defs.o -Denablemultithread -O3 -lm -lpthread gcc -Denablemultithread -O3 -c seq2regtable.c gcc -o seq2regtable mtxutl.o io.o seq2regtable.o defs.o -Denablemultithread -O3 -lm -lpthread gcc -Denablemultithread -O3 -c regtable2seq.c gcc -o regtable2seq mtxutl.o io.o regtable2seq.o defs.o mltaln9.o -Denablemultithread -O3 -lm -lpthread gcc -Denablemultithread -O3 -c score.c gcc -o score io.o mtxutl.o mltaln9.o score.o constants.o defs.o -Denablemultithread -O3 -lm -lpthread gcc -Denablemultithread -O3 -c getlag.c gcc -o getlag mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o getlag.o defs.o fft.o fftFunctions.o -Denablemultithread -O3 -lm -lpthread gcc -Denablemultithread -O3 -c dndpre.c gcc -o dndpre dndpre.o io.o constants.o mtxutl.o mltaln9.o defs.o -Denablemultithread -O3 -lm -lpthread gcc -Denablemultithread -O3 -c dndpre2.c gcc -o dndpre2 dndpre2.o io.o constants.o mtxutl.o mltaln9.o defs.o -Denablemultithread -O3 -lm -lpthread gcc -Denablemultithread -O3 -c setcore.c gcc -o setcore mtxutl.o io.o mltaln9.o tddis.o constants.o partQalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Ralignmm.o Qalignmm.o Halignmm.o Falign.o Falign_localhom.o Galign11.o SAalignmm.o MSalignmm.o setcore.o defs.o fft.o fftFunctions.o -Denablemultithread -O3 -lm -lpthread gcc -Denablemultithread -O3 -c replaceu.c gcc -o replaceu mtxutl.o io.o replaceu.o defs.o mltaln9.o -Denablemultithread -O3 -lm -lpthread gcc -Denablemultithread -O3 -c restoreu.c gcc -o restoreu mtxutl.o io.o restoreu.o defs.o mltaln9.o -Denablemultithread -O3 -lm -lpthread gcc -o version version.c -Denablemultithread -O3 sed "s:_LIBDIR:/usr/lib/mafft/lib/mafft:" mafft.tmpl > mafft sed "s:_BINDIR:/usr/lib/mafft/bin:" mafft-homologs.tmpl > mafft-homologs.rb cp mafft mafft-homologs.rb ../scripts chmod 755 ../scripts/* cp dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign pair2hat3s multi2hat3s rnatest pairash splittbfast disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre dndpre2 setcore replaceu restoreu version ../binaries chmod 755 ../binaries/* cp mafft.1 mafft-homologs.1 ../binaries done. make[2]: Leaving directory `/«PKGBUILDDIR»/core' make[1]: Leaving directory `/«PKGBUILDDIR»' dh_auto_test -a fakeroot debian/rules binary-arch dh binary-arch --with quilt dh_testroot -a dh_prep -a dh_installdirs -a dh_auto_install -a debian/rules override_dh_install make[1]: Entering directory `/«PKGBUILDDIR»' /usr/bin/make -C core PREFIX=/«PKGBUILDDIR»/debian/mafft/usr/lib/mafft MANDIR=/«PKGBUILDDIR»/debian/mafft/usr/share/man/man1 LIBDIR=/«PKGBUILDDIR»/debian/mafft/usr/lib/mafft/lib/mafft install make[2]: Entering directory `/«PKGBUILDDIR»/core' cp mafft mafft-homologs.rb ../scripts chmod 755 ../scripts/* cp dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign pair2hat3s multi2hat3s rnatest pairash splittbfast disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre dndpre2 setcore replaceu restoreu version ../binaries chmod 755 ../binaries/* cp mafft.1 mafft-homologs.1 ../binaries done. mkdir -p /«PKGBUILDDIR»/debian/mafft/usr/lib/mafft/lib/mafft chmod 755 /«PKGBUILDDIR»/debian/mafft/usr/lib/mafft/lib/mafft mkdir -p /«PKGBUILDDIR»/debian/mafft/usr/lib/mafft/bin chmod 755 /«PKGBUILDDIR»/debian/mafft/usr/lib/mafft/bin chmod 755 mafft mafft-homologs.rb install mafft mafft-homologs.rb /«PKGBUILDDIR»/debian/mafft/usr/lib/mafft/bin chmod 755 dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign pair2hat3s multi2hat3s rnatest pairash splittbfast disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre dndpre2 setcore replaceu restoreu version install dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign pair2hat3s multi2hat3s rnatest pairash splittbfast disttbfast tbfast mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre dndpre2 setcore replaceu restoreu version /«PKGBUILDDIR»/debian/mafft/usr/lib/mafft/lib/mafft install -m 644 mafft.1 mafft-homologs.1 /«PKGBUILDDIR»/debian/mafft/usr/lib/mafft/lib/mafft ( cd /«PKGBUILDDIR»/debian/mafft/usr/lib/mafft/bin; \ rm -f linsi ginsi einsi fftns fftnsi nwns nwnsi xinsi qinsi; \ rm -f mafft-linsi mafft-ginsi mafft-einsi mafft-fftns mafft-fftnsi mafft-nwns mafft-nwnsi mafft-xinsi mafft-qinsi; \ ln -s mafft linsi; ln -s mafft ginsi; ln -s mafft fftns; \ ln -s mafft fftnsi; ln -s mafft nwns; ln -s mafft nwnsi; \ ln -s mafft einsi; \ ln -s mafft mafft-linsi; ln -s mafft mafft-ginsi; ln -s mafft mafft-fftns; \ ln -s mafft mafft-fftnsi; ln -s mafft mafft-nwns; ln -s mafft mafft-nwnsi; \ ln -s mafft mafft-einsi; ln -s mafft mafft-xinsi; ln -s mafft mafft-qinsi;\ rm -f mafft-profile mafft-profile.exe; ln -s /«PKGBUILDDIR»/debian/mafft/usr/lib/mafft/lib/mafft/mafft-profile .; \ rm -f mafft-distance mafft-distance.exe; ln -s /«PKGBUILDDIR»/debian/mafft/usr/lib/mafft/lib/mafft/mafft-distance . ) mkdir -p /«PKGBUILDDIR»/debian/mafft/usr/share/man/man1 chmod 755 /«PKGBUILDDIR»/debian/mafft/usr/share/man/man1 install -m 644 mafft.1 mafft-homologs.1 /«PKGBUILDDIR»/debian/mafft/usr/share/man/man1 make[2]: Leaving directory `/«PKGBUILDDIR»/core' rm /«PKGBUILDDIR»/debian/mafft/usr/lib/mafft/lib/mafft/*.1 # Testing Mafft… MAFFT_BINARIES=/«PKGBUILDDIR»/binaries scripts/mafft test/sample | diff test/sample.fftns2 - nseq = 36 nlen = distance = sixtuples iterate = 0 cycle = 2 nthread = 0 done. scoremtx = 1 Gap Penalty = -1.53, +0.00, +0.00 Making a distance matrix .. 1 / 36 11 / 36 21 / 36 31 / 36 done. Constructing a UPGMA tree ... 0 / 36 10 / 36 20 / 36 30 / 36 done. Progressive alignment ... STEP 1 / 35 f STEP 2 / 35 f STEP 3 / 35 f STEP 4 / 35 f STEP 5 / 35 f STEP 6 / 35 f STEP 7 / 35 f STEP 8 / 35 f STEP 9 / 35 f STEP 10 / 35 f STEP 11 / 35 f STEP 12 / 35 f STEP 13 / 35 f STEP 14 / 35 f STEP 15 / 35 f STEP 16 / 35 f STEP 17 / 35 f STEP 18 / 35 f STEP 19 / 35 f STEP 20 / 35 f STEP 21 / 35 f STEP 22 / 35 f STEP 23 / 35 d STEP 24 / 35 f STEP 25 / 35 d STEP 26 / 35 f STEP 27 / 35 d STEP 28 / 35 d STEP 29 / 35 f STEP 30 / 35 d STEP 31 / 35 d STEP 32 / 35 d STEP 33 / 35 d STEP 34 / 35 d Reallocating..done. *alloclen = 2119 STEP 35 / 35 d done. disttbfast (aa) Version 6.864b alg=A, model=BLOSUM62, 1.530, -0.000, -0.000 0 thread(s) nthread = 0 blosum 62 / kimura 200 done. scoremtx = 1 Gap Penalty = -1.53, +0.00, +0.00 Making a distance matrix .. 0 / 35 10 / 35 20 / 35 30 / 35 done. Constructing a UPGMA tree ... 0 / 36 10 / 36 20 / 36 30 / 36 done. Progressive alignment ... STEP 1 /35 f STEP 2 /35 f STEP 3 /35 f STEP 4 /35 f STEP 5 /35 f STEP 6 /35 f STEP 7 /35 f STEP 8 /35 f STEP 9 /35 f STEP 10 /35 f STEP 11 /35 f STEP 12 /35 f STEP 13 /35 f STEP 14 /35 f STEP 15 /35 f STEP 16 /35 f STEP 17 /35 f STEP 18 /35 f STEP 19 /35 f STEP 20 /35 f STEP 21 /35 f STEP 22 /35 f STEP 23 /35 d STEP 24 /35 f STEP 25 /35 f STEP 26 /35 f STEP 27 /35 d STEP 28 /35 d STEP 29 /35 f STEP 30 /35 f STEP 31 /35 d STEP 32 /35 d STEP 33 /35 d STEP 34 /35 d STEP 35 /35 d done. tbfast (aa) Version 6.864b alg=A, model=BLOSUM62, 1.530, -0.000, -0.000 0 thread(s) Strategy: FFT-NS-2 (Fast but rough) Progressive method (guide trees were built 2 times.) If unsure which option to use, try 'mafft --auto input > output'. If the possibility of long gaps can be excluded, add '--ep 0.123'. For more information, see 'mafft --help', 'mafft --man' and the mafft page. MAFFT_BINARIES=/«PKGBUILDDIR»/binaries scripts/mafft --maxiterate 100 test/sample | diff test/sample.fftnsi - nseq = 36 nlen = distance = sixtuples iterate = 16 cycle = 2 nthread = 0 done. scoremtx = 1 Gap Penalty = -1.53, +0.00, +0.00 Making a distance matrix .. 1 / 36 11 / 36 21 / 36 31 / 36 done. Constructing a UPGMA tree ... 0 / 36 10 / 36 20 / 36 30 / 36 done. Progressive alignment ... STEP 1 / 35 f STEP 2 / 35 f STEP 3 / 35 f STEP 4 / 35 f STEP 5 / 35 f STEP 6 / 35 f STEP 7 / 35 f STEP 8 / 35 f STEP 9 / 35 f STEP 10 / 35 f STEP 11 / 35 f STEP 12 / 35 f STEP 13 / 35 f STEP 14 / 35 f STEP 15 / 35 f STEP 16 / 35 f STEP 17 / 35 f STEP 18 / 35 f STEP 19 / 35 f STEP 20 / 35 f STEP 21 / 35 f STEP 22 / 35 f STEP 23 / 35 d STEP 24 / 35 f STEP 25 / 35 d STEP 26 / 35 f STEP 27 / 35 d STEP 28 / 35 d STEP 29 / 35 f STEP 30 / 35 d STEP 31 / 35 d STEP 32 / 35 d STEP 33 / 35 d STEP 34 / 35 d Reallocating..done. *alloclen = 2119 STEP 35 / 35 d done. disttbfast (aa) Version 6.864b alg=A, model=BLOSUM62, 1.530, -0.000, -0.000 0 thread(s) nthread = 0 blosum 62 / kimura 200 done. scoremtx = 1 Gap Penalty = -1.53, +0.00, +0.00 Making a distance matrix .. 0 / 35 10 / 35 20 / 35 30 / 35 done. Constructing a UPGMA tree ... 0 / 36 10 / 36 20 / 36 30 / 36 done. Progressive alignment ... STEP 1 /35 f STEP 2 /35 f STEP 3 /35 f STEP 4 /35 f STEP 5 /35 f STEP 6 /35 f STEP 7 /35 f STEP 8 /35 f STEP 9 /35 f STEP 10 /35 f STEP 11 /35 f STEP 12 /35 f STEP 13 /35 f STEP 14 /35 f STEP 15 /35 f STEP 16 /35 f STEP 17 /35 f STEP 18 /35 f STEP 19 /35 f STEP 20 /35 f STEP 21 /35 f STEP 22 /35 f STEP 23 /35 d STEP 24 /35 f STEP 25 /35 f STEP 26 /35 f STEP 27 /35 d STEP 28 /35 d STEP 29 /35 f STEP 30 /35 f STEP 31 /35 d STEP 32 /35 d STEP 33 /35 d STEP 34 /35 d STEP 35 /35 d done. tbfast (aa) Version 6.864b alg=A, model=BLOSUM62, 1.530, -0.000, -0.000 0 thread(s) nthread = 0 done. scoremtx = 1 1/ 36 2/ 36 3/ 36 4/ 36 5/ 36 6/ 36 7/ 36 8/ 36 9/ 36 10/ 36 11/ 36 12/ 36 13/ 36 14/ 36 15/ 36 16/ 36 17/ 36 18/ 36 19/ 36 20/ 36 21/ 36 22/ 36 23/ 36 24/ 36 25/ 36 26/ 36 27/ 36 28/ 36 29/ 36 30/ 36 31/ 36 32/ 36 33/ 36 34/ 36 35/ 36 dndpre (aa) Version 6.864b alg=X, model=BLOSUM62, 1.530, +0.123, -0.000 0 thread(s) nthread = 0 randomseed = 0 blosum 62 / kimura 200 poffset = 0 niter = 16 done. scoremtx = 1 0 / 36 10 / 36 20 / 36 30 / 36 Segment 1/ 1 1- 712 STEP 001-001-0 identical. STEP 001-001-1 identical. STEP 001-002-0 identical. STEP 001-002-1 identical. STEP 001-003-0 identical. STEP 001-003-1 identical. STEP 001-004-0 identical. STEP 001-004-1 identical. STEP 001-005-0 identical. STEP 001-005-1 identical. STEP 001-006-0 identical. STEP 001-006-1 identical. STEP 001-007-0 rejected. STEP 001-007-1 identical. STEP 001-008-0 identical. STEP 001-008-1 identical. STEP 001-009-0 rejected. STEP 001-009-1 rejected. STEP 001-010-0 rejected. STEP 001-010-1 identical. STEP 001-011-0 identical. STEP 001-011-1 identical. STEP 001-012-0 identical. STEP 001-012-1 identical. STEP 001-013-0 identical. STEP 001-013-1 identical. STEP 001-014-0 identical. STEP 001-014-1 accepted. STEP 001-015-0 identical. STEP 001-015-1 identical. STEP 001-016-0 identical. STEP 001-016-1 accepted. STEP 001-017-0 identical. STEP 001-017-1 identical. STEP 001-018-0 identical. STEP 001-018-1 identical. STEP 001-019-0 rejected. STEP 001-019-1 rejected. STEP 001-020-0 accepted. STEP 001-020-1 rejected. STEP 001-021-0 rejected. STEP 001-021-1 rejected. STEP 001-022-0 rejected. STEP 001-022-1 rejected. STEP 001-023-0 rejected. STEP 001-023-1 identical. STEP 001-024-0 rejected. STEP 001-024-1 rejected. STEP 001-025-0 identical. STEP 001-025-1 accepted. STEP 001-026-0 identical. STEP 001-026-1 rejected. STEP 001-027-0 rejected. STEP 001-027-1 identical. STEP 001-028-0 identical. STEP 001-028-1 rejected. STEP 001-029-0 accepted. STEP 001-029-1 accepted. STEP 001-030-0 accepted. STEP 001-030-1 rejected. STEP 001-031-0 identical. STEP 001-031-1 rejected. STEP 001-032-0 rejected. STEP 001-032-1 identical. STEP 001-033-0 accepted. STEP 001-033-1 rejected. STEP 001-034-0 rejected. STEP 001-034-1 rejected. STEP 001-035-1 rejected. STEP 002-035-1 rejected. STEP 002-034-0 rejected. STEP 002-034-1 rejected. STEP 002-033-0 identical. STEP 002-033-1 rejected. STEP 002-032-0 rejected. STEP 002-032-1 identical. STEP 002-031-0 identical. STEP 002-031-1 rejected. STEP 002-030-0 accepted. STEP 002-030-1 rejected. STEP 002-029-0 rejected. STEP 002-029-1 accepted. STEP 002-028-0 identical. STEP 002-028-1 rejected. STEP 002-027-0 rejected. STEP 002-027-1 identical. STEP 002-026-0 identical. STEP 002-026-1 rejected. STEP 002-025-0 identical. STEP 002-025-1 rejected. STEP 002-024-0 rejected. STEP 002-024-1 rejected. STEP 002-023-0 rejected. STEP 002-023-1 identical. STEP 002-022-0 rejected. STEP 002-022-1 rejected. STEP 002-021-0 rejected. STEP 002-021-1 rejected. STEP 002-020-0 identical. STEP 002-020-1 rejected. STEP 002-019-0 rejected. STEP 002-019-1 rejected. STEP 002-018-0 identical. STEP 002-018-1 identical. STEP 002-017-0 identical. STEP 002-017-1 identical. STEP 002-016-0 identical. STEP 002-016-1 identical. STEP 002-015-0 identical. STEP 002-015-1 identical. STEP 002-014-0 identical. STEP 002-014-1 identical. STEP 002-013-0 identical. STEP 002-013-1 accepted. STEP 002-012-0 identical. STEP 002-012-1 identical. STEP 002-011-0 identical. STEP 002-011-1 identical. STEP 002-010-0 accepted. STEP 002-010-1 identical. STEP 002-009-0 identical. STEP 002-009-1 accepted. STEP 002-008-0 identical. STEP 002-008-1 identical. STEP 002-007-0 identical. STEP 002-007-1 identical. STEP 002-006-0 identical. STEP 002-006-1 identical. STEP 002-005-0 identical. STEP 002-005-1 identical. STEP 002-004-0 identical. STEP 002-004-1 identical. STEP 002-003-0 identical. STEP 002-003-1 identical. STEP 002-002-0 identical. STEP 002-002-1 identical. STEP 002-001-0 identical. STEP 002-001-1 identical. STEP 003-001-0 identical. STEP 003-001-1 identical. STEP 003-002-0 identical. STEP 003-002-1 identical. STEP 003-003-0 identical. STEP 003-003-1 identical. STEP 003-004-0 identical. STEP 003-004-1 identical. STEP 003-005-0 identical. STEP 003-005-1 identical. STEP 003-006-0 identical. STEP 003-006-1 identical. STEP 003-007-0 identical. STEP 003-007-1 identical. STEP 003-008-0 identical. STEP 003-008-1 identical. STEP 003-009-0 identical. STEP 003-009-1 identical. STEP 003-010-0 identical. STEP 003-010-1 identical. STEP 003-011-0 identical. STEP 003-011-1 identical. STEP 003-012-0 identical. STEP 003-012-1 identical. STEP 003-013-0 identical. STEP 003-013-1 identical. STEP 003-014-0 identical. STEP 003-014-1 identical. STEP 003-015-0 identical. STEP 003-015-1 identical. STEP 003-016-0 identical. STEP 003-016-1 identical. STEP 003-017-0 identical. STEP 003-017-1 identical. STEP 003-018-0 identical. STEP 003-018-1 identical. STEP 003-019-0 rejected. STEP 003-019-1 rejected. STEP 003-020-0 identical. STEP 003-020-1 rejected. STEP 003-021-0 rejected. STEP 003-021-1 rejected. STEP 003-022-0 rejected. STEP 003-022-1 rejected. STEP 003-023-0 rejected. STEP 003-023-1 identical. STEP 003-024-0 rejected. STEP 003-024-1 rejected. STEP 003-025-0 identical. STEP 003-025-1 rejected. STEP 003-026-0 identical. STEP 003-026-1 rejected. STEP 003-027-0 rejected. STEP 003-027-1 identical. STEP 003-028-0 identical. STEP 003-028-1 rejected. Converged. done dvtditr (aa) Version 6.864b alg=A, model=BLOSUM62, 1.530, -0.000, -0.000 0 thread(s) Strategy: FFT-NS-i (Accurate but slow) Iterative refinement method (max. 16 iterations) If unsure which option to use, try 'mafft --auto input > output'. If the possibility of long gaps can be excluded, add '--ep 0.123'. For more information, see 'mafft --help', 'mafft --man' and the mafft page. MAFFT_BINARIES=/«PKGBUILDDIR»/binaries scripts/mafft --globalpair test/sample | diff test/sample.gins1 - nseq = 36 nlen = distance = global iterate = 0 cycle = 1 nthread = 0 done. scoremtx = 1 Gap Penalty = -2.00, -0.10, +0.10 0 / 36 1 / 36 2 / 36 3 / 36 4 / 36 5 / 36 6 / 36 7 / 36 8 / 36 9 / 36 10 / 36 11 / 36 12 / 36 13 / 36 14 / 36 15 / 36 16 / 36 17 / 36 18 / 36 19 / 36 20 / 36 21 / 36 22 / 36 23 / 36 24 / 36 25 / 36 26 / 36 27 / 36 28 / 36 29 / 36 30 / 36 31 / 36 32 / 36 33 / 36 34 / 36 ##### writing hat3 pairlocalalign (aa) Version 6.864b alg=A, model=BLOSUM62, 2.000, -0.099, +0.100 0 thread(s) nthread = 0 blosum 62 / kimura 200 Loading 'hat3' ... done. done. scoremtx = 1 Gap Penalty = -1.53, +0.00, +0.00 Loading 'hat2' ... done. Constructing a UPGMA tree ... 0 / 36 10 / 36 20 / 36 30 / 36 done. Progressive alignment ... STEP 1 /35 c STEP 2 /35 c STEP 3 /35 c STEP 4 /35 c STEP 5 /35 c STEP 6 /35 c STEP 7 /35 c STEP 8 /35 c STEP 9 /35 c STEP 10 /35 c STEP 11 /35 c STEP 12 /35 c STEP 13 /35 c STEP 14 /35 c STEP 15 /35 c STEP 16 /35 c STEP 17 /35 c STEP 18 /35 c STEP 19 /35 c STEP 20 /35 c STEP 21 /35 c STEP 22 /35 c STEP 23 /35 c STEP 24 /35 c STEP 25 /35 c STEP 26 /35 c STEP 27 /35 c STEP 28 /35 c STEP 29 /35 c STEP 30 /35 c STEP 31 /35 c STEP 32 /35 c STEP 33 /35 c STEP 34 /35 c Reallocating..done. *alloclen = 2116 STEP 35 /35 c done. tbfast (aa) Version 6.864b alg=A, model=BLOSUM62, 1.530, -0.000, -0.000 0 thread(s) Strategy: G-INS-1 (Not tested.) Progressive method incorporating GLOBAL pairwise alignment information If unsure which option to use, try 'mafft --auto input > output'. If the possibility of long gaps can be excluded, add '--ep 0.123'. For more information, see 'mafft --help', 'mafft --man' and the mafft page. MAFFT_BINARIES=/«PKGBUILDDIR»/binaries scripts/mafft --globalpair --maxiterate 100 test/sample | diff test/sample.ginsi - nseq = 36 nlen = distance = global iterate = 16 cycle = 1 nthread = 0 done. scoremtx = 1 Gap Penalty = -2.00, -0.10, +0.10 0 / 36 1 / 36 2 / 36 3 / 36 4 / 36 5 / 36 6 / 36 7 / 36 8 / 36 9 / 36 10 / 36 11 / 36 12 / 36 13 / 36 14 / 36 15 / 36 16 / 36 17 / 36 18 / 36 19 / 36 20 / 36 21 / 36 22 / 36 23 / 36 24 / 36 25 / 36 26 / 36 27 / 36 28 / 36 29 / 36 30 / 36 31 / 36 32 / 36 33 / 36 34 / 36 ##### writing hat3 pairlocalalign (aa) Version 6.864b alg=A, model=BLOSUM62, 2.000, -0.099, +0.100 0 thread(s) nthread = 0 blosum 62 / kimura 200 Loading 'hat3' ... done. done. scoremtx = 1 Gap Penalty = -1.53, +0.00, +0.00 Loading 'hat2' ... done. Constructing a UPGMA tree ... 0 / 36 10 / 36 20 / 36 30 / 36 done. Progressive alignment ... STEP 1 /35 c STEP 2 /35 c STEP 3 /35 c STEP 4 /35 c STEP 5 /35 c STEP 6 /35 c STEP 7 /35 c STEP 8 /35 c STEP 9 /35 c STEP 10 /35 c STEP 11 /35 c STEP 12 /35 c STEP 13 /35 c STEP 14 /35 c STEP 15 /35 c STEP 16 /35 c STEP 17 /35 c STEP 18 /35 c STEP 19 /35 c STEP 20 /35 c STEP 21 /35 c STEP 22 /35 c STEP 23 /35 c STEP 24 /35 c STEP 25 /35 c STEP 26 /35 c STEP 27 /35 c STEP 28 /35 c STEP 29 /35 c STEP 30 /35 c STEP 31 /35 c STEP 32 /35 c STEP 33 /35 c STEP 34 /35 c Reallocating..done. *alloclen = 2116 STEP 35 /35 c done. tbfast (aa) Version 6.864b alg=A, model=BLOSUM62, 1.530, -0.000, -0.000 0 thread(s) nthread = 0 randomseed = 0 blosum 62 / kimura 200 poffset = 0 niter = 16 Loading 'hat3' ... done. done. scoremtx = 1 0 / 36 10 / 36 20 / 36 30 / 36 Segment 1/ 1 1- 710 STEP 001-001-0 identical. STEP 001-001-1 identical. STEP 001-002-0 identical. STEP 001-002-1 identical. STEP 001-003-0 identical. STEP 001-003-1 identical. STEP 001-004-0 identical. STEP 001-004-1 identical. STEP 001-005-0 identical. STEP 001-005-1 identical. STEP 001-006-0 accepted. STEP 001-006-1 accepted. STEP 001-007-0 identical. STEP 001-007-1 identical. STEP 001-008-0 identical. STEP 001-008-1 identical. STEP 001-009-0 identical. STEP 001-009-1 identical. STEP 001-010-0 identical. STEP 001-010-1 identical. STEP 001-011-0 identical. STEP 001-011-1 accepted. STEP 001-012-0 identical. STEP 001-012-1 identical. STEP 001-013-0 identical. STEP 001-013-1 accepted. STEP 001-014-0 identical. STEP 001-014-1 rejected. STEP 001-015-0 identical. STEP 001-015-1 identical. STEP 001-016-0 identical. STEP 001-016-1 identical. STEP 001-017-0 identical. STEP 001-017-1 identical. STEP 001-018-0 identical. STEP 001-018-1 identical. STEP 001-019-0 identical. STEP 001-019-1 rejected. STEP 001-020-0 accepted. STEP 001-020-1 identical. STEP 001-021-0 identical. STEP 001-021-1 identical. STEP 001-022-0 accepted. STEP 001-022-1 rejected. STEP 001-023-0 identical. STEP 001-023-1 rejected. STEP 001-024-0 accepted. STEP 001-024-1 accepted. STEP 001-025-0 accepted. STEP 001-025-1 accepted. STEP 001-026-0 identical. STEP 001-026-1 accepted. STEP 001-027-0 rejected. STEP 001-027-1 identical. STEP 001-028-0 identical. STEP 001-028-1 identical. STEP 001-029-0 accepted. STEP 001-029-1 accepted. STEP 001-030-0 rejected. STEP 001-030-1 accepted. STEP 001-031-0 identical. STEP 001-031-1 accepted. STEP 001-032-0 accepted. STEP 001-032-1 rejected. STEP 001-033-0 rejected. STEP 001-033-1 rejected. STEP 001-034-0 rejected. STEP 001-034-1 rejected. STEP 001-035-1 accepted. STEP 002-035-1 identical. STEP 002-034-0 accepted. STEP 002-034-1 rejected. STEP 002-033-0 rejected. STEP 002-033-1 rejected. STEP 002-032-0 rejected. STEP 002-032-1 rejected. STEP 002-031-0 rejected. STEP 002-031-1 accepted. STEP 002-030-0 identical. STEP 002-030-1 rejected. STEP 002-029-0 rejected. STEP 002-029-1 rejected. STEP 002-028-0 accepted. STEP 002-028-1 rejected. STEP 002-027-0 identical. STEP 002-027-1 identical. STEP 002-026-0 identical. STEP 002-026-1 identical. STEP 002-025-0 identical. STEP 002-025-1 identical. STEP 002-024-0 identical. STEP 002-024-1 accepted. STEP 002-023-0 rejected. STEP 002-023-1 identical. STEP 002-022-0 identical. STEP 002-022-1 accepted. STEP 002-021-0 identical. STEP 002-021-1 identical. STEP 002-020-0 identical. STEP 002-020-1 identical. STEP 002-019-0 identical. STEP 002-019-1 identical. STEP 002-018-0 identical. STEP 002-018-1 identical. STEP 002-017-0 accepted. STEP 002-017-1 identical. STEP 002-016-0 identical. STEP 002-016-1 identical. STEP 002-015-0 identical. STEP 002-015-1 identical. STEP 002-014-0 identical. STEP 002-014-1 accepted. STEP 002-013-0 identical. STEP 002-013-1 identical. STEP 002-012-0 identical. STEP 002-012-1 identical. STEP 002-011-0 identical. STEP 002-011-1 identical. STEP 002-010-0 identical. STEP 002-010-1 identical. STEP 002-009-0 identical. STEP 002-009-1 identical. STEP 002-008-0 identical. STEP 002-008-1 identical. STEP 002-007-0 identical. STEP 002-007-1 identical. STEP 002-006-0 rejected. STEP 002-006-1 accepted. STEP 002-005-0 identical. STEP 002-005-1 identical. STEP 002-004-0 identical. STEP 002-004-1 identical. STEP 002-003-0 identical. STEP 002-003-1 identical. STEP 002-002-0 identical. STEP 002-002-1 identical. STEP 002-001-0 identical. STEP 002-001-1 identical. STEP 003-001-0 identical. STEP 003-001-1 identical. STEP 003-002-0 identical. STEP 003-002-1 identical. STEP 003-003-0 identical. STEP 003-003-1 identical. STEP 003-004-0 identical. STEP 003-004-1 identical. STEP 003-005-0 identical. STEP 003-005-1 identical. STEP 003-006-0 rejected. STEP 003-006-1 identical. STEP 003-007-0 identical. STEP 003-007-1 identical. STEP 003-008-0 identical. STEP 003-008-1 identical. STEP 003-009-0 identical. STEP 003-009-1 identical. STEP 003-010-0 identical. STEP 003-010-1 identical. STEP 003-011-0 identical. STEP 003-011-1 identical. STEP 003-012-0 identical. STEP 003-012-1 identical. STEP 003-013-0 identical. STEP 003-013-1 identical. STEP 003-014-0 identical. STEP 003-014-1 identical. STEP 003-015-0 identical. STEP 003-015-1 identical. STEP 003-016-0 identical. STEP 003-016-1 identical. STEP 003-017-0 identical. STEP 003-017-1 identical. STEP 003-018-0 identical. STEP 003-018-1 identical. STEP 003-019-0 identical. STEP 003-019-1 identical. STEP 003-020-0 identical. STEP 003-020-1 identical. STEP 003-021-0 identical. STEP 003-021-1 identical. STEP 003-022-0 identical. STEP 003-022-1 identical. STEP 003-023-0 rejected. STEP 003-023-1 identical. STEP 003-024-0 identical. STEP 003-024-1 identical. STEP 003-025-0 identical. STEP 003-025-1 identical. STEP 003-026-0 identical. STEP 003-026-1 rejected. STEP 003-027-0 identical. STEP 003-027-1 identical. STEP 003-028-0 identical. STEP 003-028-1 rejected. STEP 003-029-0 rejected. STEP 003-029-1 rejected. STEP 003-030-0 identical. STEP 003-030-1 identical. STEP 003-031-0 rejected. STEP 003-031-1 rejected. Converged. done dvtditr (aa) Version 6.864b alg=A, model=BLOSUM62, 1.530, -0.000, -0.000 0 thread(s) Strategy: G-INS-i (Suitable for sequences of similar lengths, very slow) Iterative refinement method (<16) with GLOBAL pairwise alignment information If unsure which option to use, try 'mafft --auto input > output'. If the possibility of long gaps can be excluded, add '--ep 0.123'. For more information, see 'mafft --help', 'mafft --man' and the mafft page. MAFFT_BINARIES=/«PKGBUILDDIR»/binaries scripts/mafft --localpair test/sample | diff test/sample.lins1 - nseq = 36 nlen = distance = local iterate = 0 cycle = 1 nthread = 0 done. scoremtx = 1 Gap Penalty = -2.00, -0.10, +0.10 0 / 36 1 / 36 2 / 36 3 / 36 4 / 36 5 / 36 6 / 36 7 / 36 8 / 36 9 / 36 10 / 36 11 / 36 12 / 36 13 / 36 14 / 36 15 / 36 16 / 36 17 / 36 18 / 36 19 / 36 20 / 36 21 / 36 22 / 36 23 / 36 24 / 36 25 / 36 26 / 36 27 / 36 28 / 36 29 / 36 30 / 36 31 / 36 32 / 36 33 / 36 34 / 36 ##### writing hat3 pairlocalalign (aa) Version 6.864b alg=L, model=BLOSUM62, 2.000, -0.099, +0.100 0 thread(s) nthread = 0 blosum 62 / kimura 200 Loading 'hat3' ... done. done. scoremtx = 1 Gap Penalty = -1.53, +0.00, +0.00 Loading 'hat2' ... done. Constructing a UPGMA tree ... 0 / 36 10 / 36 20 / 36 30 / 36 done. Progressive alignment ... STEP 1 /35 c STEP 2 /35 c STEP 3 /35 c STEP 4 /35 c STEP 5 /35 c STEP 6 /35 c STEP 7 /35 c STEP 8 /35 c STEP 9 /35 c STEP 10 /35 c STEP 11 /35 c STEP 12 /35 c STEP 13 /35 c STEP 14 /35 c STEP 15 /35 c STEP 16 /35 c STEP 17 /35 c STEP 18 /35 c STEP 19 /35 c STEP 20 /35 c STEP 21 /35 c STEP 22 /35 c STEP 23 /35 c STEP 24 /35 c STEP 25 /35 c STEP 26 /35 c STEP 27 /35 c STEP 28 /35 c STEP 29 /35 c STEP 30 /35 c STEP 31 /35 c STEP 32 /35 c STEP 33 /35 c STEP 34 /35 c Reallocating..done. *alloclen = 2097 STEP 35 /35 c done. tbfast (aa) Version 6.864b alg=A, model=BLOSUM62, 1.530, -0.000, -0.000 0 thread(s) Strategy: L-INS-1 (Not tested.) Progressive method incorporating LOCAL pairwise alignment information If unsure which option to use, try 'mafft --auto input > output'. If the possibility of long gaps can be excluded, add '--ep 0.123'. For more information, see 'mafft --help', 'mafft --man' and the mafft page. MAFFT_BINARIES=/«PKGBUILDDIR»/binaries scripts/mafft --localpair --maxiterate 100 test/sample | diff test/sample.linsi - nseq = 36 nlen = distance = local iterate = 16 cycle = 1 nthread = 0 done. scoremtx = 1 Gap Penalty = -2.00, -0.10, +0.10 0 / 36 1 / 36 2 / 36 3 / 36 4 / 36 5 / 36 6 / 36 7 / 36 8 / 36 9 / 36 10 / 36 11 / 36 12 / 36 13 / 36 14 / 36 15 / 36 16 / 36 17 / 36 18 / 36 19 / 36 20 / 36 21 / 36 22 / 36 23 / 36 24 / 36 25 / 36 26 / 36 27 / 36 28 / 36 29 / 36 30 / 36 31 / 36 32 / 36 33 / 36 34 / 36 ##### writing hat3 pairlocalalign (aa) Version 6.864b alg=L, model=BLOSUM62, 2.000, -0.099, +0.100 0 thread(s) nthread = 0 blosum 62 / kimura 200 Loading 'hat3' ... done. done. scoremtx = 1 Gap Penalty = -1.53, +0.00, +0.00 Loading 'hat2' ... done. Constructing a UPGMA tree ... 0 / 36 10 / 36 20 / 36 30 / 36 done. Progressive alignment ... STEP 1 /35 c STEP 2 /35 c STEP 3 /35 c STEP 4 /35 c STEP 5 /35 c STEP 6 /35 c STEP 7 /35 c STEP 8 /35 c STEP 9 /35 c STEP 10 /35 c STEP 11 /35 c STEP 12 /35 c STEP 13 /35 c STEP 14 /35 c STEP 15 /35 c STEP 16 /35 c STEP 17 /35 c STEP 18 /35 c STEP 19 /35 c STEP 20 /35 c STEP 21 /35 c STEP 22 /35 c STEP 23 /35 c STEP 24 /35 c STEP 25 /35 c STEP 26 /35 c STEP 27 /35 c STEP 28 /35 c STEP 29 /35 c STEP 30 /35 c STEP 31 /35 c STEP 32 /35 c STEP 33 /35 c STEP 34 /35 c Reallocating..done. *alloclen = 2097 STEP 35 /35 c done. tbfast (aa) Version 6.864b alg=A, model=BLOSUM62, 1.530, -0.000, -0.000 0 thread(s) nthread = 0 randomseed = 0 blosum 62 / kimura 200 poffset = 0 niter = 16 Loading 'hat3' ... done. done. scoremtx = 1 0 / 36 10 / 36 20 / 36 30 / 36 Segment 1/ 1 1- 691 STEP 001-001-0 identical. STEP 001-001-1 identical. STEP 001-002-0 identical. STEP 001-002-1 identical. STEP 001-003-0 identical. STEP 001-003-1 identical. STEP 001-004-0 identical. STEP 001-004-1 identical. STEP 001-005-0 identical. STEP 001-005-1 identical. STEP 001-006-0 rejected. STEP 001-006-1 identical. STEP 001-007-0 identical. STEP 001-007-1 identical. STEP 001-008-0 identical. STEP 001-008-1 identical. STEP 001-009-0 identical. STEP 001-009-1 identical. STEP 001-010-0 identical. STEP 001-010-1 identical. STEP 001-011-0 identical. STEP 001-011-1 accepted. STEP 001-012-0 rejected. STEP 001-012-1 identical. STEP 001-013-0 identical. STEP 001-013-1 rejected. STEP 001-014-0 identical. STEP 001-014-1 identical. STEP 001-015-0 identical. STEP 001-015-1 identical. STEP 001-016-0 identical. STEP 001-016-1 identical. STEP 001-017-0 identical. STEP 001-017-1 identical. STEP 001-018-0 identical. STEP 001-018-1 identical. STEP 001-019-0 rejected. STEP 001-019-1 accepted. STEP 001-020-0 accepted. STEP 001-020-1 identical. STEP 001-021-0 identical. STEP 001-021-1 identical. STEP 001-022-0 rejected. STEP 001-022-1 rejected. STEP 001-023-0 rejected. STEP 001-023-1 accepted. STEP 001-024-0 rejected. STEP 001-024-1 accepted. STEP 001-025-0 identical. STEP 001-025-1 accepted. STEP 001-026-0 identical. STEP 001-026-1 rejected. STEP 001-027-0 identical. STEP 001-027-1 identical. STEP 001-028-0 rejected. STEP 001-028-1 rejected. STEP 001-029-0 accepted. STEP 001-029-1 accepted. STEP 001-030-0 rejected. STEP 001-030-1 accepted. STEP 001-031-0 rejected. STEP 001-031-1 rejected. STEP 001-032-0 accepted. STEP 001-032-1 rejected. STEP 001-033-0 accepted. STEP 001-033-1 rejected. STEP 001-034-0 rejected. STEP 001-034-1 rejected. STEP 001-035-1 accepted. STEP 002-035-1 identical. STEP 002-034-0 rejected. STEP 002-034-1 rejected. STEP 002-033-0 identical. STEP 002-033-1 rejected. STEP 002-032-0 identical. STEP 002-032-1 rejected. STEP 002-031-0 rejected. STEP 002-031-1 accepted. STEP 002-030-0 rejected. STEP 002-030-1 rejected. STEP 002-029-0 accepted. STEP 002-029-1 rejected. STEP 002-028-0 accepted. STEP 002-028-1 accepted. STEP 002-027-0 identical. STEP 002-027-1 identical. STEP 002-026-0 identical. STEP 002-026-1 accepted. STEP 002-025-0 identical. STEP 002-025-1 identical. STEP 002-024-0 accepted. STEP 002-024-1 rejected. STEP 002-023-0 accepted. STEP 002-023-1 rejected. STEP 002-022-0 accepted. STEP 002-022-1 accepted. STEP 002-021-0 identical. STEP 002-021-1 identical. STEP 002-020-0 identical. STEP 002-020-1 rejected. STEP 002-019-0 identical. STEP 002-019-1 accepted. STEP 002-018-0 identical. STEP 002-018-1 identical. STEP 002-017-0 accepted. STEP 002-017-1 identical. STEP 002-016-0 identical. STEP 002-016-1 accepted. STEP 002-015-0 identical. STEP 002-015-1 identical. STEP 002-014-0 identical. STEP 002-014-1 identical. STEP 002-013-0 identical. STEP 002-013-1 rejected. STEP 002-012-0 identical. STEP 002-012-1 identical. STEP 002-011-0 identical. STEP 002-011-1 identical. STEP 002-010-0 identical. STEP 002-010-1 identical. STEP 002-009-0 identical. STEP 002-009-1 identical. STEP 002-008-0 identical. STEP 002-008-1 identical. STEP 002-007-0 identical. STEP 002-007-1 identical. STEP 002-006-0 identical. STEP 002-006-1 identical. STEP 002-005-0 identical. STEP 002-005-1 identical. STEP 002-004-0 identical. STEP 002-004-1 identical. STEP 002-003-0 identical. STEP 002-003-1 identical. STEP 002-002-0 identical. STEP 002-002-1 identical. STEP 002-001-0 identical. STEP 002-001-1 identical. STEP 003-001-0 identical. STEP 003-001-1 identical. STEP 003-002-0 identical. STEP 003-002-1 identical. STEP 003-003-0 identical. STEP 003-003-1 identical. STEP 003-004-0 identical. STEP 003-004-1 identical. STEP 003-005-0 identical. STEP 003-005-1 identical. STEP 003-006-0 identical. STEP 003-006-1 identical. STEP 003-007-0 identical. STEP 003-007-1 identical. STEP 003-008-0 identical. STEP 003-008-1 identical. STEP 003-009-0 identical. STEP 003-009-1 identical. STEP 003-010-0 identical. STEP 003-010-1 identical. STEP 003-011-0 identical. STEP 003-011-1 identical. STEP 003-012-0 identical. STEP 003-012-1 identical. STEP 003-013-0 identical. STEP 003-013-1 rejected. STEP 003-014-0 identical. STEP 003-014-1 identical. STEP 003-015-0 identical. STEP 003-015-1 identical. STEP 003-016-0 identical. STEP 003-016-1 identical. STEP 003-017-0 identical. STEP 003-017-1 identical. STEP 003-018-0 identical. STEP 003-018-1 identical. STEP 003-019-0 identical. STEP 003-019-1 identical. STEP 003-020-0 identical. STEP 003-020-1 rejected. STEP 003-021-0 identical. STEP 003-021-1 identical. Converged. done dvtditr (aa) Version 6.864b alg=A, model=BLOSUM62, 1.530, -0.000, -0.000 0 thread(s) Strategy: L-INS-i (Probably most accurate, very slow) Iterative refinement method (<16) with LOCAL pairwise alignment information If unsure which option to use, try 'mafft --auto input > output'. If the possibility of long gaps can be excluded, add '--ep 0.123'. For more information, see 'mafft --help', 'mafft --man' and the mafft page. make[1]: Leaving directory `/«PKGBUILDDIR»' dh_installdocs -a dh_installchangelogs -a dh_installexamples -a dh_installman -a dh_installcatalogs -a dh_installcron -a dh_installdebconf -a dh_installemacsen -a dh_installifupdown -a dh_installinfo -a dh_installinit -a dh_installmenu -a dh_installmime -a dh_installmodules -a dh_installlogcheck -a dh_installlogrotate -a dh_installpam -a dh_installppp -a dh_installudev -a dh_installwm -a dh_installxfonts -a dh_installgsettings -a dh_bugfiles -a dh_ucf -a dh_lintian -a dh_gconf -a dh_icons -a dh_perl -a dh_usrlocal -a dh_link -a dh_compress -a dh_fixperms -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a debian/rules override_dh_builddeb make[1]: Entering directory `/«PKGBUILDDIR»' dh_builddeb -- -Z xz dpkg-deb: building package `mafft' in `../mafft_6.864-1_armhf.deb'. make[1]: Leaving directory `/«PKGBUILDDIR»' dpkg-genchanges -B -mbuildd >../mafft_6.864-1_armhf.changes dpkg-genchanges: arch-specific upload - not including arch-independent packages dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build mafft-6.864 dpkg-buildpackage: binary only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120601-1206 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ mafft_6.864-1_armhf.changes: ──────────────────────────── Format: 1.8 Date: Thu, 12 Jan 2012 19:00:31 +0900 Source: mafft Binary: mafft Architecture: armhf Version: 6.864-1 Distribution: testing Urgency: low Maintainer: buildd Changed-By: Charles Plessy Description: mafft - Multiple alignment program for amino acid or nucleotide sequences Changes: mafft (6.864-1) unstable; urgency=low . * New upstream release. * Pre-Depends on dpkg (>= 1.15.6) for xz compression support (debian/control). * Renamed debian/README.Debian debian/README.test. * Track the new website in debian/watch. Checksums-Sha1: 01488e17adb9d5ae3abd3797254a53900699a2bf 517130 mafft_6.864-1_armhf.deb Checksums-Sha256: 88404efbd828563f64e99c2e9a131773a7bea0db26eaf58d02e80a4661d0ccab 517130 mafft_6.864-1_armhf.deb Files: e0170b22774e9dc90275d63294201af1 517130 science optional mafft_6.864-1_armhf.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ mafft_6.864-1_armhf.deb ─────────────────────── new debian package, version 2.0. size 517130 bytes: control archive= 2137 bytes. 1395 bytes, 31 lines control 3203 bytes, 46 lines md5sums Package: mafft Version: 6.864-1 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 6036 Pre-Depends: dpkg (>= 1.15.6) Depends: libc6 (>= 2.13-28) Recommends: blast2, lynx, ruby Enhances: t-coffee Section: science Priority: optional Homepage: http://mafft.cbrc.jp/alignment/software/ Description: Multiple alignment program for amino acid or nucleotide sequences MAFFT is a multiple sequence alignment program which offers three accuracy-oriented methods: * L-INS-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information), * G-INS-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information), * E-INS-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences), and five speed-oriented methods: * FFT-NS-i (iterative refinement method; two cycles only), * FFT-NS-i (iterative refinement method; max. 1000 iterations), * FFT-NS-2 (fast; progressive method), * FFT-NS-1 (very fast; recommended for >2000 sequences; progressive method with a rough guide tree), * NW-NS-PartTree-1 (recommended for ∼50,000 sequences; progressive method with the PartTree algorithm). drwxr-xr-x root/root 0 2012-06-01 12:05 ./ drwxr-xr-x root/root 0 2012-06-01 12:06 ./usr/ drwxr-xr-x root/root 0 2012-06-01 12:06 ./usr/bin/ drwxr-xr-x root/root 0 2012-06-01 12:05 ./usr/share/ drwxr-xr-x root/root 0 2012-06-01 12:02 ./usr/share/man/ drwxr-xr-x root/root 0 2012-06-01 12:06 ./usr/share/man/man1/ -rw-r--r-- root/root 4420 2012-06-01 12:05 ./usr/share/man/man1/mafft.1.gz -rw-r--r-- root/root 2130 2012-06-01 12:05 ./usr/share/man/man1/mafft-homologs.1.gz drwxr-xr-x root/root 0 2012-06-01 12:05 ./usr/share/doc/ drwxr-xr-x root/root 0 2012-06-01 12:06 ./usr/share/doc/mafft/ -rw-r--r-- root/root 1811 2012-01-12 02:00 ./usr/share/doc/mafft/changelog.Debian.gz -rw-r--r-- root/root 1982 2012-01-12 01:40 ./usr/share/doc/mafft/copyright drwxr-xr-x root/root 0 2012-06-01 12:06 ./usr/share/doc/mafft/test/ -rw-r--r-- root/root 7203 2010-10-05 16:20 ./usr/share/doc/mafft/test/sample.fftns2.gz -rw-r--r-- root/root 6763 2007-04-04 23:00 ./usr/share/doc/mafft/test/sample.gz -rw-r--r-- root/root 1916 2007-11-28 03:15 ./usr/share/doc/mafft/test/samplerna.qinsi -rw-r--r-- root/root 7191 2009-03-16 03:14 ./usr/share/doc/mafft/test/sample.ginsi.gz -rw-r--r-- root/root 7255 2009-03-16 03:15 ./usr/share/doc/mafft/test/sample.lins1.gz -rw-r--r-- root/root 7518 2009-03-16 03:16 ./usr/share/doc/mafft/test/sample.dpparttree.gz -rw-r--r-- root/root 1916 2007-11-28 03:14 ./usr/share/doc/mafft/test/samplerna.xinsi -rw-r--r-- root/root 7257 2009-03-16 03:13 ./usr/share/doc/mafft/test/sample.gins1.gz -rw-r--r-- root/root 1502 2007-11-28 03:13 ./usr/share/doc/mafft/test/samplerna -rw-r--r-- root/root 7186 2009-03-16 03:14 ./usr/share/doc/mafft/test/sample.linsi.gz -rw-r--r-- root/root 7452 2009-03-16 03:16 ./usr/share/doc/mafft/test/sample.parttree.gz -rw-r--r-- root/root 7202 2011-03-29 14:57 ./usr/share/doc/mafft/test/sample.fftnsi.gz drwxr-xr-x root/root 0 2012-06-01 12:02 ./usr/lib/ drwxr-xr-x root/root 0 2012-06-01 12:02 ./usr/lib/mafft/ drwxr-xr-x root/root 0 2012-06-01 12:06 ./usr/lib/mafft/bin/ -rwxr-xr-x root/root 8263 2012-06-01 12:02 ./usr/lib/mafft/bin/mafft-homologs.rb -rwxr-xr-x root/root 54164 2012-06-01 12:02 ./usr/lib/mafft/bin/mafft drwxr-xr-x root/root 0 2012-06-01 12:02 ./usr/lib/mafft/lib/ drwxr-xr-x root/root 0 2012-06-01 12:06 ./usr/lib/mafft/lib/mafft/ -rwxr-xr-x root/root 214796 2012-06-01 12:06 ./usr/lib/mafft/lib/mafft/rnatest -rwxr-xr-x root/root 187180 2012-06-01 12:06 ./usr/lib/mafft/lib/mafft/dndblast -rwxr-xr-x root/root 369524 2012-06-01 12:06 ./usr/lib/mafft/lib/mafft/dvtditr -rwxr-xr-x root/root 354108 2012-06-01 12:06 ./usr/lib/mafft/lib/mafft/disttbfast -rwxr-xr-x root/root 180420 2012-06-01 12:06 ./usr/lib/mafft/lib/mafft/mccaskillwrap -rwxr-xr-x root/root 109728 2012-06-01 12:06 ./usr/lib/mafft/lib/mafft/restoreu -rwxr-xr-x root/root 333780 2012-06-01 12:06 ./usr/lib/mafft/lib/mafft/setcore -rwxr-xr-x root/root 358204 2012-06-01 12:06 ./usr/lib/mafft/lib/mafft/pairlocalalign -rwxr-xr-x root/root 57852 2012-06-01 12:06 ./usr/lib/mafft/lib/mafft/seq2regtable -rwxr-xr-x root/root 354636 2012-06-01 12:06 ./usr/lib/mafft/lib/mafft/tbfast -rwxr-xr-x root/root 109220 2012-06-01 12:06 ./usr/lib/mafft/lib/mafft/replaceu -rwxr-xr-x root/root 186172 2012-06-01 12:06 ./usr/lib/mafft/lib/mafft/mafft-distance -rwxr-xr-x root/root 177916 2012-06-01 12:06 ./usr/lib/mafft/lib/mafft/score -rwxr-xr-x root/root 186108 2012-06-01 12:06 ./usr/lib/mafft/lib/mafft/sextet5 -rwxr-xr-x root/root 358180 2012-06-01 12:06 ./usr/lib/mafft/lib/mafft/pairash -rwxr-xr-x root/root 57688 2012-06-01 12:06 ./usr/lib/mafft/lib/mafft/countlen -rwxr-xr-x root/root 333588 2012-06-01 12:06 ./usr/lib/mafft/lib/mafft/mafft-profile -rwxr-xr-x root/root 126804 2012-06-01 12:06 ./usr/lib/mafft/lib/mafft/f2cl -rwxr-xr-x root/root 195916 2012-06-01 12:06 ./usr/lib/mafft/lib/mafft/pair2hat3s -rwxr-xr-x root/root 112536 2012-06-01 12:06 ./usr/lib/mafft/lib/mafft/regtable2seq -rwxr-xr-x root/root 186396 2012-06-01 12:06 ./usr/lib/mafft/lib/mafft/dndfast7 -rwxr-xr-x root/root 195276 2012-06-01 12:06 ./usr/lib/mafft/lib/mafft/multi2hat3s -rwxr-xr-x root/root 358268 2012-06-01 12:06 ./usr/lib/mafft/lib/mafft/splittbfast -rwxr-xr-x root/root 178780 2012-06-01 12:06 ./usr/lib/mafft/lib/mafft/contrafoldwrap -rwxr-xr-x root/root 2888 2012-06-01 12:06 ./usr/lib/mafft/lib/mafft/version -rwxr-xr-x root/root 177916 2012-06-01 12:06 ./usr/lib/mafft/lib/mafft/dndpre2 -rwxr-xr-x root/root 333932 2012-06-01 12:06 ./usr/lib/mafft/lib/mafft/getlag -rwxr-xr-x root/root 177940 2012-06-01 12:06 ./usr/lib/mafft/lib/mafft/dndpre lrwxrwxrwx root/root 0 2012-06-01 12:06 ./usr/bin/mafft-homologs -> ../lib/mafft/bin/mafft-homologs.rb lrwxrwxrwx root/root 0 2012-06-01 12:06 ./usr/bin/mafft -> ../lib/mafft/bin/mafft lrwxrwxrwx root/root 0 2012-06-01 12:06 ./usr/share/man/man1/mafft-einsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2012-06-01 12:06 ./usr/share/man/man1/mafft-linsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2012-06-01 12:06 ./usr/share/man/man1/fftnsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2012-06-01 12:06 ./usr/share/man/man1/linsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2012-06-01 12:06 ./usr/share/man/man1/mafft-ginsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2012-06-01 12:06 ./usr/share/man/man1/fftns.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2012-06-01 12:06 ./usr/share/man/man1/mafft-fftnsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2012-06-01 12:06 ./usr/share/man/man1/mafft-fftns.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2012-06-01 12:06 ./usr/share/man/man1/mafft-profile.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2012-06-01 12:06 ./usr/share/man/man1/ginsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2012-06-01 12:06 ./usr/share/man/man1/einsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2012-06-01 12:06 ./usr/lib/mafft/bin/nwns -> mafft lrwxrwxrwx root/root 0 2012-06-01 12:06 ./usr/lib/mafft/bin/mafft-nwnsi -> mafft lrwxrwxrwx root/root 0 2012-06-01 12:06 ./usr/lib/mafft/bin/mafft-nwns -> mafft lrwxrwxrwx root/root 0 2012-06-01 12:06 ./usr/lib/mafft/bin/linsi -> mafft lrwxrwxrwx root/root 0 2012-06-01 12:06 ./usr/lib/mafft/bin/einsi -> mafft lrwxrwxrwx root/root 0 2012-06-01 12:06 ./usr/lib/mafft/bin/mafft-xinsi -> mafft lrwxrwxrwx root/root 0 2012-06-01 12:06 ./usr/lib/mafft/bin/mafft-einsi -> mafft lrwxrwxrwx root/root 0 2012-06-01 12:06 ./usr/lib/mafft/bin/ginsi -> mafft lrwxrwxrwx root/root 0 2012-06-01 12:06 ./usr/lib/mafft/bin/mafft-fftns -> mafft lrwxrwxrwx root/root 0 2012-06-01 12:06 ./usr/lib/mafft/bin/mafft-qinsi -> mafft lrwxrwxrwx root/root 0 2012-06-01 12:06 ./usr/lib/mafft/bin/mafft-ginsi -> mafft lrwxrwxrwx root/root 0 2012-06-01 12:06 ./usr/lib/mafft/bin/mafft-distance -> ../lib/mafft/mafft-distance lrwxrwxrwx root/root 0 2012-06-01 12:06 ./usr/lib/mafft/bin/mafft-profile -> ../lib/mafft/mafft-profile lrwxrwxrwx root/root 0 2012-06-01 12:06 ./usr/lib/mafft/bin/fftns -> mafft lrwxrwxrwx root/root 0 2012-06-01 12:06 ./usr/lib/mafft/bin/mafft-linsi -> mafft lrwxrwxrwx root/root 0 2012-06-01 12:06 ./usr/lib/mafft/bin/fftnsi -> mafft lrwxrwxrwx root/root 0 2012-06-01 12:06 ./usr/lib/mafft/bin/nwnsi -> mafft lrwxrwxrwx root/root 0 2012-06-01 12:06 ./usr/lib/mafft/bin/mafft-fftnsi -> mafft ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 0 to remove and 8 not upgraded. Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bsdmainutils* debhelper* diffstat* file* gettext* gettext-base* groff-base* html2text* intltool-debian* libcroco3* libffi5* libglib2.0-0* libmagic1* libpcre3* libpipeline1* libunistring0* libxml2* man-db* po-debconf* quilt* sbuild-build-depends-core-dummy* sbuild-build-depends-mafft-dummy* 0 upgraded, 0 newly installed, 22 to remove and 8 not upgraded. After this operation, 25.1 MB disk space will be freed. (Reading database ... 12121 files and directories currently installed.) Removing sbuild-build-depends-mafft-dummy ... Removing quilt ... Purging configuration files for quilt ... Removing debhelper ... Removing man-db ... Purging configuration files for man-db ... Removing bsdmainutils ... Purging configuration files for bsdmainutils ... Removing diffstat ... Removing file ... Removing po-debconf ... Removing intltool-debian ... Removing gettext ... Removing gettext-base ... Removing groff-base ... Purging configuration files for groff-base ... Removing html2text ... Purging configuration files for html2text ... Removing libcroco3:armhf ... Purging configuration files for libcroco3:armhf ... Removing libglib2.0-0:armhf ... Purging configuration files for libglib2.0-0:armhf ... Removing libffi5:armhf ... Purging configuration files for libffi5:armhf ... Removing libmagic1:armhf ... Purging configuration files for libmagic1:armhf ... Removing libpcre3:armhf ... Purging configuration files for libpcre3:armhf ... Removing libpipeline1:armhf ... Purging configuration files for libpipeline1:armhf ... Removing libunistring0:armhf ... Purging configuration files for libunistring0:armhf ... Removing libxml2:armhf ... Purging configuration files for libxml2:armhf ... Removing sbuild-build-depends-core-dummy ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: armhf Build-Space: 24096 Build-Time: 574 Distribution: testing Install-Time: 66 Job: mafft_6.864-1 Package: mafft Package-Time: 698 Source-Version: 6.864-1 Space: 24096 Status: successful Version: 6.864-1 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120601-1206 Build needed 00:11:38, 24096k disc space