RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: 3.2.0-37-generic #58-Ubuntu SMP Thu Jan 24 15:28:10 UTC 2013 x86_64 Buildd toolchain package versions: launchpad-buildd_114-0~53~0.IS.08.04 python-lpbuildd_114-0~53~0.IS.08.04 bzr_2.5.1-0ubuntu2. Syncing the system clock with the buildd NTP service... 17 Jul 10:47:12 ntpdate[22270]: adjust time server 10.211.37.1 offset -0.001025 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', '5d2a6dc963d721587589db108f03484968e1ef24', '/home/buildd/filecache-default/889964717cf16a5a101bdf5220b4d4f2f75cc8e0'] Unpacking chroot for build 5d2a6dc963d721587589db108f03484968e1ef24 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', '5d2a6dc963d721587589db108f03484968e1ef24'] Mounting chroot for build 5d2a6dc963d721587589db108f03484968e1ef24 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', '5d2a6dc963d721587589db108f03484968e1ef24', 'deb http://ftpmaster.internal/ubuntu saucy main universe', 'deb http://ftpmaster.internal/ubuntu saucy-security main universe', 'deb http://ftpmaster.internal/ubuntu saucy-updates main universe', 'deb http://ftpmaster.internal/ubuntu saucy-proposed main universe'] Overriding sources.list in build-5d2a6dc963d721587589db108f03484968e1ef24 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', '5d2a6dc963d721587589db108f03484968e1ef24', 'i386'] Updating debian chroot for build 5d2a6dc963d721587589db108f03484968e1ef24 Ign http://ftpmaster.internal saucy InRelease Ign http://archive-team.internal saucy InRelease Ign http://ftpmaster.internal saucy-security InRelease Ign http://ftpmaster.internal saucy-updates InRelease Ign http://archive-team.internal saucy Release.gpg Ign http://ftpmaster.internal saucy-proposed InRelease Get:1 http://archive-team.internal saucy Release [721 B] Get:2 http://ftpmaster.internal saucy Release.gpg [933 B] Get:3 http://ftpmaster.internal saucy-security Release.gpg [933 B] Get:4 http://ftpmaster.internal saucy-updates Release.gpg [933 B] Get:5 http://ftpmaster.internal saucy-proposed Release.gpg [933 B] Get:6 http://ftpmaster.internal saucy Release [40.8 kB] Get:7 http://ftpmaster.internal saucy-security Release [40.8 kB] Get:8 http://ftpmaster.internal saucy-updates Release [40.8 kB] Get:9 http://archive-team.internal saucy/main i386 Packages Get:10 http://ftpmaster.internal saucy-proposed Release [40.8 kB] Ign http://archive-team.internal saucy/main Translation-en Get:11 http://ftpmaster.internal saucy/main i386 Packages [1223 kB] Get:12 http://ftpmaster.internal saucy/universe i386 Packages [5593 kB] Get:13 http://ftpmaster.internal saucy/main Translation-en [702 kB] Get:14 http://ftpmaster.internal saucy/universe Translation-en [3851 kB] Get:15 http://ftpmaster.internal saucy-security/main i386 Packages [14 B] Get:16 http://ftpmaster.internal saucy-security/universe i386 Packages [14 B] Get:17 http://ftpmaster.internal saucy-security/main Translation-en [14 B] Get:18 http://ftpmaster.internal saucy-security/universe Translation-en [14 B] Get:19 http://ftpmaster.internal saucy-updates/main i386 Packages [14 B] Get:20 http://ftpmaster.internal saucy-updates/universe i386 Packages [14 B] Get:21 http://ftpmaster.internal saucy-updates/main Translation-en [14 B] Get:22 http://ftpmaster.internal saucy-updates/universe Translation-en [14 B] Get:23 http://ftpmaster.internal saucy-proposed/main i386 Packages [23.9 kB] Get:24 http://ftpmaster.internal saucy-proposed/universe i386 Packages [140 kB] Get:25 http://ftpmaster.internal saucy-proposed/main Translation-en [14.6 kB] Get:26 http://ftpmaster.internal saucy-proposed/universe Translation-en [90.1 kB] Fetched 11.8 MB in 6s (1885 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: libjson-c2 The following packages will be upgraded: libdbus-1-3 libjson0 libssl1.0.0 linux-libc-dev 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 2100 kB of archives. After this operation, 33.8 kB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libssl1.0.0 libdbus-1-3 libjson-c2 libjson0 linux-libc-dev Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ saucy-proposed/main libssl1.0.0 i386 1.0.1e-3ubuntu1 [990 kB] Get:2 http://ftpmaster.internal/ubuntu/ saucy/main libdbus-1-3 i386 1.6.12-0ubuntu2 [151 kB] Get:3 http://ftpmaster.internal/ubuntu/ saucy/main libjson-c2 i386 0.11-2ubuntu1 [23.9 kB] Get:4 http://ftpmaster.internal/ubuntu/ saucy/main libjson0 i386 0.11-2ubuntu1 [1012 B] Get:5 http://ftpmaster.internal/ubuntu/ saucy/main linux-libc-dev i386 3.10.0-3.12 [934 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 2100 kB in 0s (11.6 MB/s) (Reading database ... 12107 files and directories currently installed.) Preparing to replace libssl1.0.0:i386 1.0.1e-2ubuntu1.1 (using .../libssl1.0.0_1.0.1e-3ubuntu1_i386.deb) ... Unpacking replacement libssl1.0.0:i386 ... Preparing to replace libdbus-1-3:i386 1.6.12-0ubuntu1 (using .../libdbus-1-3_1.6.12-0ubuntu2_i386.deb) ... Unpacking replacement libdbus-1-3:i386 ... Selecting previously unselected package libjson-c2:i386. Unpacking libjson-c2:i386 (from .../libjson-c2_0.11-2ubuntu1_i386.deb) ... Preparing to replace libjson0:i386 0.10-1.2ubuntu2 (using .../libjson0_0.11-2ubuntu1_i386.deb) ... Unpacking replacement libjson0:i386 ... Preparing to replace linux-libc-dev:i386 3.10.0-2.11 (using .../linux-libc-dev_3.10.0-3.12_i386.deb) ... Unpacking replacement linux-libc-dev:i386 ... Setting up libssl1.0.0:i386 (1.0.1e-3ubuntu1) ... Setting up libdbus-1-3:i386 (1.6.12-0ubuntu2) ... Setting up libjson-c2:i386 (0.11-2ubuntu1) ... Setting up libjson0:i386 (0.11-2ubuntu1) ... Setting up linux-libc-dev:i386 (3.10.0-3.12) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', '5d2a6dc963d721587589db108f03484968e1ef24', 'i386', 'saucy-proposed', '--nolog', '--batch', '--archive=ubuntu', '--dist=saucy-proposed', '-A', '--purpose=PRIMARY', '--architecture=i386', '--comp=universe', 'wise_2.4.1-14.dsc'] Initiating build 5d2a6dc963d721587589db108f03484968e1ef24 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 3.2.0-37-generic #58-Ubuntu SMP Thu Jan 24 15:28:10 UTC 2013 i686 Automatic build of wise_2.4.1-14 on batsu by sbuild/i386 1.170.5 Build started at 20130717-1047 ****************************************************************************** wise_2.4.1-14.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 8), dpkg-dev (>= 1.16.1~), quilt, texlive-latex-base, texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev Checking for already installed source dependencies... debhelper: missing dpkg-dev: already installed (1.16.10ubuntu3 >= 1.16.1~ is satisfied) quilt: missing texlive-latex-base: missing texlive-extra-utils: missing hevea: missing docbook-to-man: missing libglib2.0-dev: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install debhelper quilt texlive-latex-base texlive-extra-utils hevea docbook-to-man libglib2.0-dev Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: apparmor-easyprof apparmor-easyprof-ubuntu bsdmainutils dh-apparmor diffstat docbook file fontconfig-config fonts-dejavu-core gettext gettext-base ghostscript groff-base gsfonts intltool-debian libasprintf-dev libasprintf0c2 libavahi-client3 libavahi-common-data libavahi-common3 libcairo2 libcroco3 libcups2 libcupsfilters1 libcupsimage2 libelfg0 libexpat1 libffi6 libfontconfig1 libfreetype6 libgettextpo-dev libgettextpo0 libglib2.0-0 libglib2.0-bin libglib2.0-data libgraphite2-3 libgs9 libgs9-common libice6 libicu48 libijs-0.35 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libkpathsea6 liblcms2-2 libmagic1 libnetpbm10 libpaper-utils libpaper1 libpcre3-dev libpcrecpp0 libpipeline1 libpixman-1-0 libpoppler37 libpopt0 libptexenc1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.3-minimal libpython3.3-stdlib libsm6 libsp1c2 libtiff5 libunistring0 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxml2 libxmu6 libxpm4 libxrender1 libxt6 luatex man-db mime-support netpbm ocaml-base-nox pkg-config po-debconf poppler-data python python-minimal python2.7 python2.7-minimal python3 python3-minimal python3.3 python3.3-minimal sgml-base sgml-data sp tex-common texlive-base texlive-binaries ttf-dejavu-core ucf x11-common xdg-utils xml-core zlib1g-dev Suggested packages: wamerican wordlist whois vacation dh-make docbook-defguide docbook-dsssl docbook-xml psgml gettext-doc ghostscript-cups ghostscript-x hpijs groff hevea-doc cups-common libglib2.0-doc fonts-droid liblcms2-utils less www-browser libmail-box-perl poppler-utils fonts-japanese-mincho fonts-ipafont-mincho fonts-japanese-gothic fonts-ipafont-gothic fonts-arphic-ukai fonts-arphic-uming fonts-unfonts-core python-doc python-tk python2.7-doc binfmt-support python3-doc python3-tk python3.3-doc procmail graphviz default-mta mail-transport-agent sgml-base-doc perlsgml w3-recs opensp libxml2-utils doc-base perl-tk gv postscript-viewer xpdf-reader pdf-viewer purifyeps chktex latexmk dvipng xindy dvidvi fragmaster lacheck latexdiff gvfs-bin Recommended packages: curl wget lynx-cur shared-mime-info texlive-luatex libmail-sendmail-perl lmodern ruby wish texlive-latex-recommended texlive-latex-base-doc libfile-mimeinfo-perl x11-utils x11-xserver-utils The following NEW packages will be installed: apparmor-easyprof apparmor-easyprof-ubuntu bsdmainutils debhelper dh-apparmor diffstat docbook docbook-to-man file fontconfig-config fonts-dejavu-core gettext gettext-base ghostscript groff-base gsfonts hevea intltool-debian libasprintf-dev libasprintf0c2 libavahi-client3 libavahi-common-data libavahi-common3 libcairo2 libcroco3 libcups2 libcupsfilters1 libcupsimage2 libelfg0 libexpat1 libffi6 libfontconfig1 libfreetype6 libgettextpo-dev libgettextpo0 libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev libgraphite2-3 libgs9 libgs9-common libice6 libicu48 libijs-0.35 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libkpathsea6 liblcms2-2 libmagic1 libnetpbm10 libpaper-utils libpaper1 libpcre3-dev libpcrecpp0 libpipeline1 libpixman-1-0 libpoppler37 libpopt0 libptexenc1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.3-minimal libpython3.3-stdlib libsm6 libsp1c2 libtiff5 libunistring0 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxml2 libxmu6 libxpm4 libxrender1 libxt6 luatex man-db mime-support netpbm ocaml-base-nox pkg-config po-debconf poppler-data python python-minimal python2.7 python2.7-minimal python3 python3-minimal python3.3 python3.3-minimal quilt sgml-base sgml-data sp tex-common texlive-base texlive-binaries texlive-extra-utils texlive-latex-base ttf-dejavu-core ucf x11-common xdg-utils xml-core zlib1g-dev 0 upgraded, 117 newly installed, 0 to remove and 0 not upgraded. Need to get 79.1 MB of archives. After this operation, 243 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libexpat1 libffi6 libmagic1 libpopt0 libpython3.3-minimal mime-support libpython3.3-stdlib python3.3-minimal libasprintf0c2 libglib2.0-0 libpipeline1 libxau6 libxdmcp6 libxcb1 libx11-data libx11-6 libxext6 libxml2 groff-base bsdmainutils man-db sgml-base ucf fonts-dejavu-core ttf-dejavu-core fontconfig-config libavahi-common-data libavahi-common3 libavahi-client3 libfreetype6 libfontconfig1 libpixman-1-0 libxcb-render0 libxcb-shm0 libxrender1 libcairo2 libcroco3 libcups2 libjpeg-turbo8 libjpeg8 libjbig0 libtiff5 libcupsfilters1 libcupsimage2 libelfg0 libunistring0 libgettextpo0 libgraphite2-3 x11-common libice6 libicu48 liblcms2-2 libpaper1 libpcrecpp0 libpoppler37 libsm6 libxt6 libxmu6 libxpm4 libxaw7 poppler-data libpython2.7-minimal python2.7-minimal file libpython3-stdlib python3.3 python3-minimal python3 gettext-base libglib2.0-data xml-core apparmor-easyprof-ubuntu libasprintf-dev libgettextpo-dev gettext intltool-debian po-debconf apparmor-easyprof dh-apparmor debhelper diffstat sgml-data docbook libsp1c2 sp docbook-to-man libijs-0.35 libjbig2dec0 libgs9-common libgs9 gsfonts ghostscript libnetpbm10 netpbm xdg-utils tex-common libpaper-utils libkpathsea6 libptexenc1 texlive-binaries luatex texlive-base ocaml-base-nox hevea libglib2.0-bin libpcre3-dev pkg-config zlib1g-dev libglib2.0-dev libpython2.7-stdlib libpython-stdlib python2.7 python-minimal python quilt texlive-latex-base texlive-extra-utils Authentication warning overridden. Get:1 http://ftpmaster.internal/ubuntu/ saucy/main libexpat1 i386 2.1.0-4 [127 kB] Get:2 http://ftpmaster.internal/ubuntu/ saucy/main libffi6 i386 3.0.13-2ubuntu1 [16.0 kB] Get:3 http://ftpmaster.internal/ubuntu/ saucy/main libmagic1 i386 5.11-2ubuntu4 [172 kB] Get:4 http://ftpmaster.internal/ubuntu/ saucy/main libpopt0 i386 1.16-7ubuntu3 [29.4 kB] Get:5 http://ftpmaster.internal/ubuntu/ saucy/main libpython3.3-minimal i386 3.3.2-3ubuntu1 [582 kB] Get:6 http://ftpmaster.internal/ubuntu/ saucy/main mime-support all 3.54ubuntu1 [31.7 kB] Get:7 http://ftpmaster.internal/ubuntu/ saucy/main libpython3.3-stdlib i386 3.3.2-3ubuntu1 [2677 kB] Get:8 http://ftpmaster.internal/ubuntu/ saucy/main python3.3-minimal i386 3.3.2-3ubuntu1 [1675 kB] Get:9 http://ftpmaster.internal/ubuntu/ saucy/main libasprintf0c2 i386 0.18.1.1-10ubuntu3 [6700 B] Get:10 http://ftpmaster.internal/ubuntu/ saucy/main libglib2.0-0 i386 2.37.3-1ubuntu2 [994 kB] Get:11 http://ftpmaster.internal/ubuntu/ saucy/main libpipeline1 i386 1.2.4-1 [26.5 kB] Get:12 http://ftpmaster.internal/ubuntu/ saucy/main libxau6 i386 1:1.0.8-1 [8352 B] Get:13 http://ftpmaster.internal/ubuntu/ saucy/main libxdmcp6 i386 1:1.1.1-1 [13.1 kB] Get:14 http://ftpmaster.internal/ubuntu/ saucy/main libxcb1 i386 1.8.1-2ubuntu3 [48.2 kB] Get:15 http://ftpmaster.internal/ubuntu/ saucy/main libx11-data all 2:1.5.0-1ubuntu2 [180 kB] Get:16 http://ftpmaster.internal/ubuntu/ saucy/main libx11-6 i386 2:1.5.0-1ubuntu2 [771 kB] Get:17 http://ftpmaster.internal/ubuntu/ saucy/main libxext6 i386 2:1.3.2-1 [33.9 kB] Get:18 http://ftpmaster.internal/ubuntu/ saucy/main libxml2 i386 2.9.1+dfsg1-2ubuntu1 [672 kB] Get:19 http://ftpmaster.internal/ubuntu/ saucy/main groff-base i386 1.22.2-3 [705 kB] Get:20 http://ftpmaster.internal/ubuntu/ saucy/main bsdmainutils i386 9.0.5ubuntu1 [197 kB] Get:21 http://ftpmaster.internal/ubuntu/ saucy/main man-db i386 2.6.5-2 [704 kB] Get:22 http://ftpmaster.internal/ubuntu/ saucy/main sgml-base all 1.26+nmu4ubuntu1 [12.5 kB] Get:23 http://ftpmaster.internal/ubuntu/ saucy/main ucf all 3.0027+nmu1 [56.3 kB] Get:24 http://ftpmaster.internal/ubuntu/ saucy/main fonts-dejavu-core all 2.33+svn2514-3ubuntu1 [1019 kB] Get:25 http://ftpmaster.internal/ubuntu/ saucy/main ttf-dejavu-core all 2.33+svn2514-3ubuntu1 [2964 B] Get:26 http://ftpmaster.internal/ubuntu/ saucy/main fontconfig-config all 2.10.93-0ubuntu1 [50.5 kB] Get:27 http://ftpmaster.internal/ubuntu/ saucy/main libavahi-common-data i386 0.6.31-2ubuntu2 [22.2 kB] Get:28 http://ftpmaster.internal/ubuntu/ saucy/main libavahi-common3 i386 0.6.31-2ubuntu2 [25.8 kB] Get:29 http://ftpmaster.internal/ubuntu/ saucy/main libavahi-client3 i386 0.6.31-2ubuntu2 [29.5 kB] Get:30 http://ftpmaster.internal/ubuntu/ saucy/main libfreetype6 i386 2.4.12-0ubuntu1 [351 kB] Get:31 http://ftpmaster.internal/ubuntu/ saucy/main libfontconfig1 i386 2.10.93-0ubuntu1 [142 kB] Get:32 http://ftpmaster.internal/ubuntu/ saucy/main libpixman-1-0 i386 0.28.2-0ubuntu1 [250 kB] Get:33 http://ftpmaster.internal/ubuntu/ saucy/main libxcb-render0 i386 1.8.1-2ubuntu3 [14.2 kB] Get:34 http://ftpmaster.internal/ubuntu/ saucy/main libxcb-shm0 i386 1.8.1-2ubuntu3 [5764 B] Get:35 http://ftpmaster.internal/ubuntu/ saucy/main libxrender1 i386 1:0.9.8-1 [20.3 kB] Get:36 http://ftpmaster.internal/ubuntu/ saucy/main libcairo2 i386 1.12.14-0ubuntu1 [643 kB] Get:37 http://ftpmaster.internal/ubuntu/ saucy/main libcroco3 i386 0.6.8-2 [81.2 kB] Get:38 http://ftpmaster.internal/ubuntu/ saucy/main libcups2 i386 1.6.2-10 [190 kB] Get:39 http://ftpmaster.internal/ubuntu/ saucy/main libjpeg-turbo8 i386 1.2.1-0ubuntu2 [120 kB] Get:40 http://ftpmaster.internal/ubuntu/ saucy/main libjpeg8 i386 8c-2ubuntu8 [2188 B] Get:41 http://ftpmaster.internal/ubuntu/ saucy/main libjbig0 i386 2.0-2ubuntu1 [28.0 kB] Get:42 http://ftpmaster.internal/ubuntu/ saucy/main libtiff5 i386 4.0.2-4ubuntu3 [167 kB] Get:43 http://ftpmaster.internal/ubuntu/ saucy/main libcupsfilters1 i386 1.0.34-3 [74.3 kB] Get:44 http://ftpmaster.internal/ubuntu/ saucy/main libcupsimage2 i386 1.6.2-10 [17.0 kB] Get:45 http://ftpmaster.internal/ubuntu/ saucy/main libelfg0 i386 0.8.13-4~1 [46.9 kB] Get:46 http://ftpmaster.internal/ubuntu/ saucy/main libunistring0 i386 0.9.3-5build1 [430 kB] Get:47 http://ftpmaster.internal/ubuntu/ saucy/main libgettextpo0 i386 0.18.1.1-10ubuntu3 [120 kB] Get:48 http://ftpmaster.internal/ubuntu/ saucy/main libgraphite2-3 i386 1.2.3-1 [58.5 kB] Get:49 http://ftpmaster.internal/ubuntu/ saucy/main x11-common all 1:7.7+1ubuntu5 [58.7 kB] Get:50 http://ftpmaster.internal/ubuntu/ saucy/main libice6 i386 2:1.0.8-2 [45.9 kB] Get:51 http://ftpmaster.internal/ubuntu/ saucy/main libicu48 i386 4.8.1.1-12 [4769 kB] Get:52 http://ftpmaster.internal/ubuntu/ saucy/main liblcms2-2 i386 2.4-0ubuntu3 [158 kB] Get:53 http://ftpmaster.internal/ubuntu/ saucy/main libpaper1 i386 1.1.24+nmu2ubuntu2 [14.4 kB] Get:54 http://ftpmaster.internal/ubuntu/ saucy/main libpcrecpp0 i386 1:8.31-2 [17.1 kB] Get:55 http://ftpmaster.internal/ubuntu/ saucy/main libpoppler37 i386 0.22.4-0ubuntu1 [845 kB] Get:56 http://ftpmaster.internal/ubuntu/ saucy/main libsm6 i386 2:1.2.1-2 [17.3 kB] Get:57 http://ftpmaster.internal/ubuntu/ saucy/main libxt6 i386 1:1.1.3-1+deb7u1 [176 kB] Get:58 http://ftpmaster.internal/ubuntu/ saucy/main libxmu6 i386 2:1.1.1-1 [52.9 kB] Get:59 http://ftpmaster.internal/ubuntu/ saucy/main libxpm4 i386 1:3.5.10-1 [38.2 kB] Get:60 http://ftpmaster.internal/ubuntu/ saucy/main libxaw7 i386 2:1.0.11-1 [196 kB] Get:61 http://ftpmaster.internal/ubuntu/ saucy/main poppler-data all 0.4.6-4 [1479 kB] Get:62 http://ftpmaster.internal/ubuntu/ saucy/main libpython2.7-minimal i386 2.7.5-5ubuntu1 [500 kB] Get:63 http://ftpmaster.internal/ubuntu/ saucy/main python2.7-minimal i386 2.7.5-5ubuntu1 [1436 kB] Get:64 http://ftpmaster.internal/ubuntu/ saucy/main file i386 5.11-2ubuntu4 [18.0 kB] Get:65 http://ftpmaster.internal/ubuntu/ saucy/main libpython3-stdlib i386 3.3.1-0ubuntu1 [8228 B] Get:66 http://ftpmaster.internal/ubuntu/ saucy/main python3.3 i386 3.3.2-3ubuntu1 [123 kB] Get:67 http://ftpmaster.internal/ubuntu/ saucy/main python3-minimal i386 3.3.1-0ubuntu1 [12.3 kB] Get:68 http://ftpmaster.internal/ubuntu/ saucy/main python3 i386 3.3.1-0ubuntu1 [50.3 kB] Get:69 http://ftpmaster.internal/ubuntu/ saucy/main gettext-base i386 0.18.1.1-10ubuntu3 [55.0 kB] Get:70 http://ftpmaster.internal/ubuntu/ saucy/main libglib2.0-data all 2.37.3-1ubuntu2 [102 kB] Get:71 http://ftpmaster.internal/ubuntu/ saucy/main xml-core all 0.13+nmu2 [23.3 kB] Get:72 http://ftpmaster.internal/ubuntu/ saucy/main apparmor-easyprof-ubuntu all 1.0.6 [5040 B] Get:73 http://ftpmaster.internal/ubuntu/ saucy/main libasprintf-dev i386 0.18.1.1-10ubuntu3 [4396 B] Get:74 http://ftpmaster.internal/ubuntu/ saucy/main libgettextpo-dev i386 0.18.1.1-10ubuntu3 [149 kB] Get:75 http://ftpmaster.internal/ubuntu/ saucy/main gettext i386 0.18.1.1-10ubuntu3 [990 kB] Get:76 http://ftpmaster.internal/ubuntu/ saucy/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:77 http://ftpmaster.internal/ubuntu/ saucy/main po-debconf all 1.0.16+nmu2ubuntu1 [210 kB] Get:78 http://ftpmaster.internal/ubuntu/ saucy-proposed/main apparmor-easyprof all 2.8.0-0ubuntu22 [22.1 kB] Get:79 http://ftpmaster.internal/ubuntu/ saucy-proposed/main dh-apparmor all 2.8.0-0ubuntu22 [7722 B] Get:80 http://ftpmaster.internal/ubuntu/ saucy/main debhelper all 9.20130630ubuntu1 [629 kB] Get:81 http://ftpmaster.internal/ubuntu/ saucy/main diffstat i386 1.56-1 [23.7 kB] Get:82 http://ftpmaster.internal/ubuntu/ saucy/main sgml-data all 2.0.9-1 [277 kB] Get:83 http://ftpmaster.internal/ubuntu/ saucy/main docbook all 4.5-5.1ubuntu1 [443 kB] Get:84 http://ftpmaster.internal/ubuntu/ saucy/main libsp1c2 i386 1.3.4-1.2.1-47.1ubuntu2 [1423 kB] Get:85 http://ftpmaster.internal/ubuntu/ saucy/main sp i386 1.3.4-1.2.1-47.1ubuntu2 [159 kB] Get:86 http://ftpmaster.internal/ubuntu/ saucy/main docbook-to-man i386 1:2.0.0-31 [80.3 kB] Get:87 http://ftpmaster.internal/ubuntu/ saucy/main libijs-0.35 i386 0.35-8build1 [17.1 kB] Get:88 http://ftpmaster.internal/ubuntu/ saucy/main libjbig2dec0 i386 0.11+20120125-1ubuntu1 [48.1 kB] Get:89 http://ftpmaster.internal/ubuntu/ saucy/main libgs9-common all 9.07~dfsg2-0ubuntu3 [2145 kB] Get:90 http://ftpmaster.internal/ubuntu/ saucy/main libgs9 i386 9.07~dfsg2-0ubuntu3 [2533 kB] Get:91 http://ftpmaster.internal/ubuntu/ saucy/main gsfonts all 1:8.11+urwcyr1.0.7~pre44-4.2ubuntu1 [3374 kB] Get:92 http://ftpmaster.internal/ubuntu/ saucy/main ghostscript i386 9.07~dfsg2-0ubuntu3 [45.1 kB] Get:93 http://ftpmaster.internal/ubuntu/ saucy/main libnetpbm10 i386 2:10.0-15ubuntu2 [65.6 kB] Get:94 http://ftpmaster.internal/ubuntu/ saucy/main netpbm i386 2:10.0-15ubuntu2 [1220 kB] Get:95 http://ftpmaster.internal/ubuntu/ saucy/main xdg-utils all 1.1.0~rc1-2ubuntu7 [65.6 kB] Get:96 http://ftpmaster.internal/ubuntu/ saucy/main tex-common all 4.04 [621 kB] Get:97 http://ftpmaster.internal/ubuntu/ saucy/main libpaper-utils i386 1.1.24+nmu2ubuntu2 [8978 B] Get:98 http://ftpmaster.internal/ubuntu/ saucy/main libkpathsea6 i386 2013.20130529.30792-1build1 [71.1 kB] Get:99 http://ftpmaster.internal/ubuntu/ saucy/main libptexenc1 i386 2013.20130529.30792-1build1 [38.4 kB] Get:100 http://ftpmaster.internal/ubuntu/ saucy/main texlive-binaries i386 2013.20130529.30792-1build1 [5917 kB] Get:101 http://ftpmaster.internal/ubuntu/ saucy/main luatex i386 0.76.0-3 [3552 kB] Get:102 http://ftpmaster.internal/ubuntu/ saucy/main texlive-base all 2013.20130530-1 [16.2 MB] Get:103 http://ftpmaster.internal/ubuntu/ saucy/main ocaml-base-nox i386 3.12.1-4ubuntu1 [581 kB] Get:104 http://ftpmaster.internal/ubuntu/ saucy/main hevea all 2.06-2 [482 kB] Get:105 http://ftpmaster.internal/ubuntu/ saucy/main libglib2.0-bin i386 2.37.3-1ubuntu2 [34.0 kB] Get:106 http://ftpmaster.internal/ubuntu/ saucy/main libpcre3-dev i386 1:8.31-2 [261 kB] Get:107 http://ftpmaster.internal/ubuntu/ saucy/main pkg-config i386 0.26-1ubuntu4 [40.5 kB] Get:108 http://ftpmaster.internal/ubuntu/ saucy/main zlib1g-dev i386 1:1.2.8.dfsg-1ubuntu1 [181 kB] Get:109 http://ftpmaster.internal/ubuntu/ saucy/main libglib2.0-dev i386 2.37.3-1ubuntu2 [1248 kB] Get:110 http://ftpmaster.internal/ubuntu/ saucy/main libpython2.7-stdlib i386 2.7.5-5ubuntu1 [2451 kB] Get:111 http://ftpmaster.internal/ubuntu/ saucy/main libpython-stdlib i386 2.7.5-1ubuntu1 [7572 B] Get:112 http://ftpmaster.internal/ubuntu/ saucy/main python2.7 i386 2.7.5-5ubuntu1 [189 kB] Get:113 http://ftpmaster.internal/ubuntu/ saucy/main python-minimal i386 2.7.5-1ubuntu1 [31.3 kB] Get:114 http://ftpmaster.internal/ubuntu/ saucy/main python i386 2.7.5-1ubuntu1 [169 kB] Get:115 http://ftpmaster.internal/ubuntu/ saucy/main quilt all 0.60-8 [286 kB] Get:116 http://ftpmaster.internal/ubuntu/ saucy/main texlive-latex-base all 2013.20130530-1 [827 kB] Get:117 http://ftpmaster.internal/ubuntu/ saucy/main texlive-extra-utils all 2013.20130530-1 [8140 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 79.1 MB in 7s (9891 kB/s) Selecting previously unselected package libexpat1:i386. 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Selecting previously unselected package python2.7. Unpacking python2.7 (from .../python2.7_2.7.5-5ubuntu1_i386.deb) ... Selecting previously unselected package python-minimal. Unpacking python-minimal (from .../python-minimal_2.7.5-1ubuntu1_i386.deb) ... Selecting previously unselected package python. Unpacking python (from .../python_2.7.5-1ubuntu1_i386.deb) ... Selecting previously unselected package quilt. Unpacking quilt (from .../archives/quilt_0.60-8_all.deb) ... Selecting previously unselected package texlive-latex-base. Unpacking texlive-latex-base (from .../texlive-latex-base_2013.20130530-1_all.deb) ... Selecting previously unselected package texlive-extra-utils. Unpacking texlive-extra-utils (from .../texlive-extra-utils_2013.20130530-1_all.deb) ... Setting up libexpat1:i386 (2.1.0-4) ... Setting up libffi6:i386 (3.0.13-2ubuntu1) ... Setting up libmagic1:i386 (5.11-2ubuntu4) ... Setting up libpopt0:i386 (1.16-7ubuntu3) ... Setting up libpython3.3-minimal:i386 (3.3.2-3ubuntu1) ... Setting up mime-support (3.54ubuntu1) ... update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode Setting up libpython3.3-stdlib:i386 (3.3.2-3ubuntu1) ... Setting up python3.3-minimal (3.3.2-3ubuntu1) ... Setting up libasprintf0c2:i386 (0.18.1.1-10ubuntu3) ... Setting up libglib2.0-0:i386 (2.37.3-1ubuntu2) ... No schema files found: doing nothing. Setting up libpipeline1:i386 (1.2.4-1) ... Setting up libxau6:i386 (1:1.0.8-1) ... Setting up libxdmcp6:i386 (1:1.1.1-1) ... Setting up libxcb1:i386 (1.8.1-2ubuntu3) ... Setting up libx11-data (2:1.5.0-1ubuntu2) ... Setting up libx11-6:i386 (2:1.5.0-1ubuntu2) ... Setting up libxext6:i386 (2:1.3.2-1) ... Setting up libxml2:i386 (2.9.1+dfsg1-2ubuntu1) ... Setting up groff-base (1.22.2-3) ... Setting up bsdmainutils (9.0.5ubuntu1) ... 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 man-db (2.6.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up sgml-base (1.26+nmu4ubuntu1) ... Setting up ucf (3.0027+nmu1) ... Setting up fonts-dejavu-core (2.33+svn2514-3ubuntu1) ... Setting up ttf-dejavu-core (2.33+svn2514-3ubuntu1) ... Setting up fontconfig-config (2.10.93-0ubuntu1) ... Setting up libavahi-common-data:i386 (0.6.31-2ubuntu2) ... Setting up libavahi-common3:i386 (0.6.31-2ubuntu2) ... Setting up libavahi-client3:i386 (0.6.31-2ubuntu2) ... Setting up libfreetype6:i386 (2.4.12-0ubuntu1) ... Setting up libfontconfig1:i386 (2.10.93-0ubuntu1) ... Setting up libpixman-1-0:i386 (0.28.2-0ubuntu1) ... Setting up libxcb-render0:i386 (1.8.1-2ubuntu3) ... Setting up libxcb-shm0:i386 (1.8.1-2ubuntu3) ... Setting up libxrender1:i386 (1:0.9.8-1) ... Setting up libcairo2:i386 (1.12.14-0ubuntu1) ... Setting up libcroco3:i386 (0.6.8-2) ... Setting up libcups2:i386 (1.6.2-10) ... Setting up libjpeg-turbo8:i386 (1.2.1-0ubuntu2) ... Setting up libjpeg8:i386 (8c-2ubuntu8) ... Setting up libjbig0:i386 (2.0-2ubuntu1) ... Setting up libtiff5:i386 (4.0.2-4ubuntu3) ... Setting up libcupsfilters1:i386 (1.0.34-3) ... Setting up libcupsimage2:i386 (1.6.2-10) ... Setting up libelfg0:i386 (0.8.13-4~1) ... Setting up libunistring0:i386 (0.9.3-5build1) ... Setting up libgettextpo0:i386 (0.18.1.1-10ubuntu3) ... Setting up libgraphite2-3:i386 (1.2.3-1) ... Setting up x11-common (1:7.7+1ubuntu5) ... invoke-rc.d: policy-rc.d denied execution of start. Setting up libice6:i386 (2:1.0.8-2) ... Setting up libicu48:i386 (4.8.1.1-12) ... Setting up liblcms2-2:i386 (2.4-0ubuntu3) ... Setting up libpaper1:i386 (1.1.24+nmu2ubuntu2) ... Creating config file /etc/papersize with new version Setting up libpcrecpp0:i386 (1:8.31-2) ... Setting up libpoppler37:i386 (0.22.4-0ubuntu1) ... Setting up libsm6:i386 (2:1.2.1-2) ... Setting up libxt6:i386 (1:1.1.3-1+deb7u1) ... Setting up libxmu6:i386 (2:1.1.1-1) ... Setting up libxpm4:i386 (1:3.5.10-1) ... Setting up libxaw7:i386 (2:1.0.11-1) ... Setting up poppler-data (0.4.6-4) ... Setting up libpython2.7-minimal:i386 (2.7.5-5ubuntu1) ... Setting up python2.7-minimal (2.7.5-5ubuntu1) ... Linking and byte-compiling packages for runtime python2.7... Setting up file (5.11-2ubuntu4) ... Setting up libpython3-stdlib:i386 (3.3.1-0ubuntu1) ... Setting up python3.3 (3.3.2-3ubuntu1) ... Setting up python3-minimal (3.3.1-0ubuntu1) ... Setting up python3 (3.3.1-0ubuntu1) ... running python rtupdate hooks for python3.3... running python post-rtupdate hooks for python3.3... Setting up gettext-base (0.18.1.1-10ubuntu3) ... Setting up libglib2.0-data (2.37.3-1ubuntu2) ... Setting up xml-core (0.13+nmu2) ... Setting up apparmor-easyprof-ubuntu (1.0.6) ... Setting up libasprintf-dev:i386 (0.18.1.1-10ubuntu3) ... Setting up libgettextpo-dev:i386 (0.18.1.1-10ubuntu3) ... Setting up gettext (0.18.1.1-10ubuntu3) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2ubuntu1) ... Setting up apparmor-easyprof (2.8.0-0ubuntu22) ... Setting up dh-apparmor (2.8.0-0ubuntu22) ... Setting up debhelper (9.20130630ubuntu1) ... Setting up diffstat (1.56-1) ... Setting up libsp1c2 (1.3.4-1.2.1-47.1ubuntu2) ... Setting up sp (1.3.4-1.2.1-47.1ubuntu2) ... Setting up libijs-0.35 (0.35-8build1) ... Setting up libjbig2dec0 (0.11+20120125-1ubuntu1) ... Setting up libgs9-common (9.07~dfsg2-0ubuntu3) ... update-alternatives: using /usr/share/ghostscript/9.07 to provide /usr/share/ghostscript/current (ghostscript-current) in auto mode Setting up libgs9 (9.07~dfsg2-0ubuntu3) ... Setting up gsfonts (1:8.11+urwcyr1.0.7~pre44-4.2ubuntu1) ... Setting up ghostscript (9.07~dfsg2-0ubuntu3) ... Setting up libnetpbm10 (2:10.0-15ubuntu2) ... Setting up netpbm (2:10.0-15ubuntu2) ... Setting up xdg-utils (1.1.0~rc1-2ubuntu7) ... Setting up tex-common (4.04) ... Running mktexlsr. This may take some time... done. texlive-base is not ready, delaying updmap-sys call texlive-base is not ready, skipping fmtutil-sys --all call Setting up libpaper-utils (1.1.24+nmu2ubuntu2) ... Setting up libkpathsea6 (2013.20130529.30792-1build1) ... Setting up libptexenc1 (2013.20130529.30792-1build1) ... Setting up texlive-binaries (2013.20130529.30792-1build1) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Building format(s) --refresh. This may take some time... done. Setting up luatex (0.76.0-3) ... texlive-base is not ready, cannot create formats Setting up texlive-base (2013.20130530-1) ... mktexlsr: /usr/share/texlive/texmf: not a directory, skipping. /usr/bin/tl-paper: setting paper size for dvips to a4. /usr/bin/tl-paper: setting paper size for dvipdfmx to a4. /usr/bin/tl-paper: setting paper size for xdvi to a4. /usr/bin/tl-paper: setting paper size for pdftex to a4. Running mktexlsr. This may take some time... done. Building format(s) --all. This may take some time... done. Setting up ocaml-base-nox (3.12.1-4ubuntu1) ... Setting up libglib2.0-bin (2.37.3-1ubuntu2) ... Setting up libpcre3-dev:i386 (1:8.31-2) ... Setting up pkg-config (0.26-1ubuntu4) ... Setting up zlib1g-dev:i386 (1:1.2.8.dfsg-1ubuntu1) ... Setting up libglib2.0-dev (2.37.3-1ubuntu2) ... Setting up libpython2.7-stdlib:i386 (2.7.5-5ubuntu1) ... Setting up libpython-stdlib:i386 (2.7.5-1ubuntu1) ... Setting up python2.7 (2.7.5-5ubuntu1) ... Setting up python-minimal (2.7.5-1ubuntu1) ... Setting up python (2.7.5-1ubuntu1) ... Setting up quilt (0.60-8) ... Processing triggers for tex-common ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Setting up hevea (2.06-2) ... Setting up texlive-latex-base (2013.20130530-1) ... Running mktexlsr. This may take some time... done. Building format(s) --all --cnffile /etc/texmf/fmt.d/10texlive-latex-base.cnf. This may take some time... done. Processing triggers for tex-common ... Running mktexlsr. This may take some time... done. Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Setting up texlive-extra-utils (2013.20130530-1) ... Processing triggers for sgml-base ... Setting up sgml-data (2.0.9-1) ... Processing triggers for sgml-base ... Setting up docbook (4.5-5.1ubuntu1) ... Processing triggers for sgml-base ... Setting up docbook-to-man (1:2.0.0-31) ... Processing triggers for libc-bin ... ldconfig deferred processing now taking place Processing triggers for tex-common ... Running mktexlsr. This may take some time... done. Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.17-0ubuntu5 make_3.81-8.2ubuntu3 dpkg-dev_1.16.10ubuntu3 gcc-4.8_4.8.1-6ubuntu1 g++-4.8_4.8.1-6ubuntu1 binutils_2.23.52.20130620-1ubuntu1 libstdc++-4.8-dev_4.8.1-6ubuntu1 libstdc++6_4.8.1-6ubuntu1 ------------------------------------------------------------------------------ dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt gpgv: Signature made Mon Jul 15 16:58:02 2013 UTC using DSA key ID EB88E930 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./wise_2.4.1-14.dsc dpkg-source: info: extracting wise in wise-2.4.1 dpkg-source: info: unpacking wise_2.4.1.orig.tar.gz dpkg-source: info: unpacking wise_2.4.1-14.debian.tar.gz dpkg-source: info: applying 01_welcome-csh.patch dpkg-source: info: applying 02_isnumber.patch dpkg-source: info: applying 03_doc-nodycache.patch dpkg-source: info: applying 04_wise2-pdflatex-update.patch dpkg-source: info: applying 05_glib2.patch dpkg-source: info: applying 06_getline.patch dpkg-source: info: applying 07_ld--as-needed.patch dpkg-source: info: applying 08_mayhem.patch dpkg-buildpackage: source package wise dpkg-buildpackage: source version 2.4.1-14 dpkg-source --before-build wise-2.4.1 dpkg-buildpackage: host architecture i386 /usr/bin/fakeroot debian/rules clean dh clean dh_testdir dh_auto_clean debian/rules override_dh_clean make[1]: Entering directory `/build/buildd/wise-2.4.1' /usr/bin/make -C src clean make[2]: Entering directory `/build/buildd/wise-2.4.1/src' cd external ; /usr/bin/make clean make[3]: Entering directory `/build/buildd/wise-2.4.1/src/external' (cd mott; make clean) make[4]: Entering directory `/build/buildd/wise-2.4.1/src/external/mott' rm -f *.[oa] make[4]: Leaving directory `/build/buildd/wise-2.4.1/src/external/mott' make[3]: Leaving directory `/build/buildd/wise-2.4.1/src/external' if test -d dynlibsrc; then cd dynlibsrc ; rm -f *.[oa]; fi if test -d models; then cd models ; rm -f *.[oa]; fi if test -d base; then cd base ; rm -f *.[oa]; fi if test -d socket; then cd socket ; rm -f *.[oa]; fi if test -d dnaindex; then cd dnaindex ; rm -f *.[oa]; fi if test -d network; then cd network ; rm -f *.[oa]; fi if test -d dyc; then cd dyc ; rm -f *.[oa]; fi if test -d HMMer2; then cd HMMer2 ; rm -f *.[oa]; fi if test -d perl; then cd perl/Wise2/libs ; rm -f *.[oa]; fi if test -x perl/Wise2/Makefile; then cd perl/Wise2/ ; /usr/bin/make clean; fi if test -d oldbin; then rm -rf oldbin; fi if test -d bin; then echo 'moving binaries to oldbin'; mv -f bin oldbin; fi make[2]: Leaving directory `/build/buildd/wise-2.4.1/src' /usr/bin/make -C debian/manpages.d clean make[2]: Entering directory `/build/buildd/wise-2.4.1/debian/manpages.d' rm -f dba.1 dnal.1 estwise.1 estwisedb.1 genewise.1 genewisedb.1 genomewise.1 promoterwise.1 psw.1 pswdb.1 scanwise.1 scanwise_server.1 make[2]: Leaving directory `/build/buildd/wise-2.4.1/debian/manpages.d' rm -f -r src/oldbin for i in dba psw dnal genomewise pswdb scanwise estwise genewise sywise genewisedb promoterwise pseudowise estwisedb; do rm -f src/models/$i; done rm -f src/network/scanwise_server rm -f docs/temp.tex rm -f docs/api.* rm -f docs/wise2.image.tex rm -f docs/*.pdf rm -f docs/*.aux rm -f docs/*.log rm -f docs/*.toc rm -f docs/*.pdf rm -f docs/*.dvi rm -f docs/*.ps rm -f docs/*.4ct rm -f docs/*.4tc rm -f docs/*.css rm -f docs/*.idv rm -f docs/*.lg rm -f docs/*.tmp rm -f docs/*.xref rm -f docs/*.haux rm -f docs/*.htoc rm -f docs/*.html rm -f -r docs/api rm -f -r docs/dynamite rm -f -r docs/wise2 dh_clean rm -f debian/wise.substvars rm -f debian/wise.*.debhelper rm -rf debian/wise/ rm -f debian/wise-doc.substvars rm -f debian/wise-doc.*.debhelper rm -rf debian/wise-doc/ rm -f debian/wise-data.substvars rm -f debian/wise-data.*.debhelper rm -rf debian/wise-data/ rm -f debian/*.debhelper.log rm -f debian/files find . \( \( -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} \; \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \) rm -f *-stamp make[1]: Leaving directory `/build/buildd/wise-2.4.1' debian/rules build dh build dh_testdir dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory `/build/buildd/wise-2.4.1' /usr/bin/make -C src all make[2]: Entering directory `/build/buildd/wise-2.4.1/src' (cd base ; /usr/bin/make CC="cc" CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c `pkg-config --cflags glib-2.0`" libwisebase.a ) make[3]: Entering directory `/build/buildd/wise-2.4.1/src/base' cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include wiseconfig.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include wisestring.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include wiseerror.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include wisememman.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include wisefile.c wisefile.dy: In function 'Wise2_myfclose': wisefile.dy:72:3: warning: format '%d' expects argument of type 'int', but argument 3 has type 'struct FILE *' [-Wformat=] fprintf(stderr,"Closing %d\n",ofp); ^ cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include wiserandom.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include wisetime.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include wiseoverlay.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include wisestreaminterface.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include commandline.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include linesubs.c ar ru libwisebase.a wiseconfig.o wisestring.o wiseerror.o wisememman.o wisefile.o wiserandom.o wisetime.o wiseoverlay.o wisestreaminterface.o commandline.o linesubs.o ar: creating libwisebase.a if test -x /bin/ranlib; then /bin/ranlib libwisebase.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisebase.a; else exit 0; fi make[3]: Leaving directory `/build/buildd/wise-2.4.1/src/base' (cd HMMer2 ; /usr/bin/make CC="cc" CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c `pkg-config --cflags glib-2.0`" libhmmer.a ) make[3]: Entering directory `/build/buildd/wise-2.4.1/src/HMMer2' cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c alphabet.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c core_algorithms.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c debug.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c emit.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c emulation.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c histogram.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c hmmio.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c mathsupport.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c masks.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c misc.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c modelmakers.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c plan7.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c plan9.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c prior.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c tophits.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c trace.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c aligneval.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c alignio.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c cluster.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c dayhoff.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c file.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c getopt.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c gnuregex.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c interleaved.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c iupac.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c msf.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c revcomp.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c selex.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c sqerror.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c sqio.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c sre_ctype.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c sre_math.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c sre_string.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c stack.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c translate.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c types.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -c weight.c ar rcv libhmmer.a alphabet.o core_algorithms.o debug.o emit.o emulation.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o prior.o tophits.o trace.o aligneval.o alignio.o cluster.o dayhoff.o file.o getopt.o gnuregex.o interleaved.o iupac.o msf.o revcomp.o selex.o sqerror.o sqio.o sre_ctype.o sre_math.o sre_string.o stack.o translate.o types.o weight.o a - alphabet.o a - core_algorithms.o a - debug.o a - emit.o a - emulation.o a - histogram.o a - hmmio.o a - mathsupport.o a - masks.o a - misc.o a - modelmakers.o a - plan7.o a - plan9.o a - prior.o a - tophits.o a - trace.o a - aligneval.o a - alignio.o a - cluster.o a - dayhoff.o a - file.o a - getopt.o a - gnuregex.o a - interleaved.o a - iupac.o a - msf.o a - revcomp.o a - selex.o a - sqerror.o a - sqio.o a - sre_ctype.o a - sre_math.o a - sre_string.o a - stack.o a - translate.o a - types.o a - weight.o if test -x /bin/ranlib; then /bin/ranlib libhmmer.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libhmmer.a; else exit 0; fi if test -x ranlib; then ranlib libhmmer.a; else exit 0; fi chmod 644 libhmmer.a make[3]: Leaving directory `/build/buildd/wise-2.4.1/src/HMMer2' (cd dynlibsrc ; /usr/bin/make CC="cc" CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c `pkg-config --cflags glib-2.0`" libdyna.a ) make[3]: Entering directory `/build/buildd/wise-2.4.1/src/dynlibsrc' cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ packaln.c packaln.dy: In function 'Wise2_read_simple_PackAln': packaln.dy:88:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(buffer,MAXLINE,ifp); ^ cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ aln.c aln.dy: In function 'Wise2_mapped_ascii_AlnBlock': aln.dy:867:7: warning: too many arguments for format [-Wformat-extra-args] fprintf(ofp," {%3.2f} ",(double)(*score_to_double)(cuml),cuml); ^ cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ dnamatrix.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ probability.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ alnrange.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ alnconvert.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ basematrix.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ shattermatrix.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ matrixdebug.c matrixdebug.dy: In function 'Wise2_user_DebugMatrix': matrixdebug.dy:208:10: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(buffer,MAXLINE,in); ^ cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ dpenvelope.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ dbsearchimpl.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ dprunimpl.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ complexsequence.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ complexevalset.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ complexconsensi.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ sequence.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ sequencestream.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ seqalign.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ hitlist.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ hsp.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ hspstream.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ codon.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ compmat.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ codonmatrix.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ codonmapper.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ sequencedb.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ hscore.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ seqlookup.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ arrayseqlookup.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ genericindexresult.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ linkedlist_lookpos.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ singlenumberspace.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ histogram.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ searchstatinterface.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ searchstatlookup.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ proteindb.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ protein.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ pairbase.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ pairbaseseq.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ genomicdb.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ randommodel.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ randomdb.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ genomic.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ cdna.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ cdnadb.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ dna.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ embl.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ genomicregion.c genomicregion.dy: In function 'Wise2_read_EMBL_FT_into_GenomicRegion': genomicregion.dy:756:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(buffer,maxlen,ifp); ^ cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ gene.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ transcript.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ translation.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ btcanvas.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ asciibtcanvas.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ dynlibcross.c ar ru libdyna.a packaln.o aln.o dnamatrix.o probability.o alnrange.o alnconvert.o basematrix.o shattermatrix.o matrixdebug.o dpenvelope.o dbsearchimpl.o dprunimpl.o complexsequence.o complexevalset.o complexconsensi.o sequence.o sequencestream.o seqalign.o hitlist.o hsp.o hspstream.o codon.o compmat.o codonmatrix.o codonmapper.o sequencedb.o hscore.o seqlookup.o arrayseqlookup.o genericindexresult.o linkedlist_lookpos.o singlenumberspace.o histogram.o searchstatinterface.o searchstatlookup.o proteindb.o protein.o pairbase.o pairbaseseq.o genomicdb.o randommodel.o randomdb.o genomic.o cdna.o cdnadb.o dna.o embl.o genomicregion.o gene.o transcript.o translation.o btcanvas.o asciibtcanvas.o dynlibcross.o ar: creating libdyna.a if test -x /bin/ranlib; then /bin/ranlib libdyna.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna.a; else exit 0; fi make[3]: Leaving directory `/build/buildd/wise-2.4.1/src/dynlibsrc' (cd dynlibsrc ; /usr/bin/make CC="cc" CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c `pkg-config --cflags glib-2.0`" libdyna_glib.a ) make[3]: Entering directory `/build/buildd/wise-2.4.1/src/dynlibsrc' cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ subseqhash.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ intallocator.c intallocator.dy: In function 'Wise2_show_allocator_status_IntAllocator': intallocator.dy:216:3: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'unsigned int' [-Wformat=] fprintf(ofp,"%d blocks allocated, using %ld bytes\n",ia->current_allocated_block,ia->current_allocated_block * (sizeof(IntAllocatorHeader)+(sizeof(int)*ia->size)) * IntAllocator_BLOCKSIZE); ^ cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ proteinstreamedindex.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ shadowseq.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ shadowseqindex.c shadowseqindex.dy: In function 'Wise2_dump_stats_ShadowSequenceIndex': shadowseqindex.dy:285:3: warning: format '%f' expects argument of type 'double', but argument 4 has type 'unsigned int' [-Wformat=] fprintf(ofp,"Head memory %d [%.2f Mbytes]\n",total_head,(total_head*sizeof(ShadowArraySeqHead))/100000); ^ cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ hsphandler.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ hspscaninterface.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ hsp2hitscan.c hsp2hitscan.dy: In function 'Wise2_one_off_two_hit_HSPscan_query_direct': hsp2hitscan.dy:214:4: warning: format '%d' expects argument of type 'int', but argument 3 has type '__time_t' [-Wformat=] ); ^ hsp2hitscan.dy:214:4: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] hsp2hitscan.dy:214:4: warning: format '%d' expects argument of type 'int', but argument 5 has type '__time_t' [-Wformat=] hsp2hitscan.dy:214:4: warning: format '%d' expects argument of type 'int', but argument 6 has type 'long int' [-Wformat=] hsp2hitscan.dy:278:4: warning: format '%d' expects argument of type 'int', but argument 3 has type '__time_t' [-Wformat=] ); ^ hsp2hitscan.dy:278:4: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] hsp2hitscan.dy:278:4: warning: format '%d' expects argument of type 'int', but argument 5 has type '__time_t' [-Wformat=] hsp2hitscan.dy:278:4: warning: format '%d' expects argument of type 'int', but argument 6 has type 'long int' [-Wformat=] hsp2hitscan.dy:291:4: warning: format '%d' expects argument of type 'int', but argument 3 has type '__time_t' [-Wformat=] ); ^ hsp2hitscan.dy:291:4: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] hsp2hitscan.dy:291:4: warning: format '%d' expects argument of type 'int', but argument 5 has type '__time_t' [-Wformat=] hsp2hitscan.dy:291:4: warning: format '%d' expects argument of type 'int', but argument 6 has type 'long int' [-Wformat=] hsp2hitscan.dy:307:4: warning: format '%d' expects argument of type 'int', but argument 3 has type '__time_t' [-Wformat=] ); ^ hsp2hitscan.dy:307:4: warning: format '%d' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] hsp2hitscan.dy:307:4: warning: format '%d' expects argument of type 'int', but argument 5 has type '__time_t' [-Wformat=] hsp2hitscan.dy:307:4: warning: format '%d' expects argument of type 'int', but argument 6 has type 'long int' [-Wformat=] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ hsplookupscan.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ hsplookupthreaded.c hsplookupthreaded.dy: In function 'Wise2_one_off_ordered_HSPscan_scan_query_direct': hsplookupthreaded.dy:263:3: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] fprintf(stderr,"retrieved array with %d elements\n",current_oph); ^ cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ hspthreadeddb.c hspthreadeddb.dy: In function 'Wise2_threadeddb_scan_worker': hspthreadeddb.dy:154:3: warning: format '%d' expects argument of type 'int', but argument 3 has type 'struct Wise2_HSPDatabaseSegment *' [-Wformat=] fprintf(stderr,"For segment %d, finished query with %d (%d) linear\n",seg,(int)seg->lm,seg->lm->len); ^ cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ hspscanruntime.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ hsptwohitscan.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ proteinindexcons.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ dnaindexcons.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ staticseq.c ar ru libdyna_glib.a subseqhash.o intallocator.o proteinstreamedindex.o shadowseq.o shadowseqindex.o hsphandler.o hspscaninterface.o hsp2hitscan.o hsplookupscan.o hsplookupthreaded.o hspthreadeddb.o hspscanruntime.o hsptwohitscan.o proteinindexcons.o dnaindexcons.o staticseq.o ar: creating libdyna_glib.a if test -x /bin/ranlib; then /bin/ranlib libdyna_glib.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna_glib.a; else exit 0; fi make[3]: Leaving directory `/build/buildd/wise-2.4.1/src/dynlibsrc' (cd external ; /usr/bin/make CC="cc" CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c `pkg-config --cflags glib-2.0`" all ) make[3]: Entering directory `/build/buildd/wise-2.4.1/src/external' (cd mott; make CC="cc" CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include " all) make[4]: Entering directory `/build/buildd/wise-2.4.1/src/external/mott' cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -D_FORTIFY_SOURCE=2 -c -o mott_api.o mott_api.c mott_api.c: In function 'InitPvaluesMott': mott_api.c:64:3: warning: incompatible implicit declaration of built-in function 'free' [enabled by default] free(freq0); ^ mott_api.c: In function 'SW_PValueMott': mott_api.c:104:7: warning: incompatible implicit declaration of built-in function 'free' [enabled by default] free(freqA); ^ mott_api.c: In function 'KarlinAltschulStatistics2': mott_api.c:144:5: warning: incompatible implicit declaration of built-in function 'free' [enabled by default] free(h+hmin); ^ mott_api.c:155:5: warning: incompatible implicit declaration of built-in function 'free' [enabled by default] free(h+hmin); ^ mott_api.c: In function 'GetHistogram': mott_api.c:179:16: warning: incompatible implicit declaration of built-in function 'calloc' [enabled by default] h = (double*)calloc(*hmax-*hmin+1,sizeof(double))-*hmin; ^ mott_api.c: In function 'RobinsonResidueFrequencies2': mott_api.c:230:27: warning: incompatible implicit declaration of built-in function 'calloc' [enabled by default] double *freq = (double*)calloc(256, sizeof(double)); ^ cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -D_FORTIFY_SOURCE=2 -c -o gaplib.o gaplib.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../../dynlibsrc -I../../base wise2_mott_bridge.c ar ru libmott.a mott_api.o gaplib.o wise2_mott_bridge.o ar: creating libmott.a if test -x /bin/ranlib; then /bin/ranlib libmott.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libmott.a; else exit 0; fi make[4]: Leaving directory `/build/buildd/wise-2.4.1/src/external/mott' make[3]: Leaving directory `/build/buildd/wise-2.4.1/src/external' (cd socket ; /usr/bin/make CC="cc" CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c `pkg-config --cflags glib-2.0`" libwisesocket.a ) make[3]: Entering directory `/build/buildd/wise-2.4.1/src/socket' cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ functionserver.c functionserver.dy: In function 'Wise2_main_loop_forking_FunctionServer': functionserver.dy:129:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(new_socket,buf,9); ^ functionserver.dy:141:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(new_socket,buf,6); ^ functionserver.dy:183:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(new_socket,buf,5); ^ cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ functionclient.c functionclient.dy: In function 'Wise2_new_FunctionProxyCoordinator': functionclient.dy:193:3: warning: passing argument 2 of 'connect' from incompatible pointer type [enabled by default] connect(out->socket, &server, sizeof(server)); ^ In file included from functionclient.c:7:0: /usr/include/i386-linux-gnu/sys/socket.h:138:12: note: expected 'const struct sockaddr *' but argument is of type 'struct sockaddr_in *' extern int connect (int __fd, __CONST_SOCKADDR_ARG __addr, socklen_t __len); ^ cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ anonobj.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ transferinterface.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ directsocketwrite.c ar ru libwisesocket.a functionserver.o functionclient.o anonobj.o transferinterface.o directsocketwrite.o ar: creating libwisesocket.a if test -x /bin/ranlib; then /bin/ranlib libwisesocket.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisesocket.a; else exit 0; fi make[3]: Leaving directory `/build/buildd/wise-2.4.1/src/socket' (cd dnaindex ; /usr/bin/make CC="cc" CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c `pkg-config --cflags glib-2.0`" all ) make[3]: Entering directory `/build/buildd/wise-2.4.1/src/dnaindex' cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly.c kmer_assembly.dy: In function 'Wise2_show_KmerAssemblyNode': kmer_assembly.dy:296:3: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t' [-Wformat=] fprintf(ofp,"Node %ld of sequence %s \n",node->number,buffer); ^ kmer_assembly.dy:302:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'kmer_t' [-Wformat=] fprintf(ofp," ... prev ... %c, %d to %ld\n",node->prev[i]->base,node->prev[i]->sequence_label_len,node->prev[i]->prev->number); ^ kmer_assembly.dy:309:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'kmer_t' [-Wformat=] fprintf(ofp," ... next ... %c, %d to %ld\n",node->next[i]->base,node->next[i]->sequence_label_len,node->next[i]->next->number); ^ kmer_assembly.dy: In function 'Wise2_remove_sequence_label_KmerAssemblyLink': kmer_assembly.dy:365:3: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'struct KmerAssemblyLink *' [-Wformat=] fprintf(stderr," ...unable to remove label %ld from link %ld (%d labels)\n",label,kal,kal->sequence_label_len); ^ kmer_assembly.dy:367:5: warning: format '%d' expects a matching 'int' argument [-Wformat=] fprintf(stderr," [%ld] is %d label\n",kal->sequence_label[i]); ^ cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_index_interface.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_direct.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_hash.c kmer_hash.dy: In function 'Wise2_free_KmerHashIndex': kmer_hash.dy:318:3: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'kmer_t' [-Wformat=] fprintf(stderr, "min_kmer: %016lx\n", khi->min_kmer); ^ kmer_hash.dy:319:3: warning: format '%lx' expects argument of type 'long unsigned int', but argument 3 has type 'kmer_t' [-Wformat=] fprintf(stderr, "max_kmer: %016lx\n", khi->max_kmer); ^ cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_count.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_glib_index.c kmer_glib_index.dy: In function 'Wise2_retrieve_by_kmer_KmerGlibIndex': kmer_glib_index.dy:77:48: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] return (void*) g_hash_table_lookup(kgi->hash,(gconstpointer)kmer); ^ kmer_glib_index.dy: In function 'Wise2_insert_by_kmer_KmerGlibIndex': kmer_glib_index.dy:84:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] g_hash_table_insert(kgi->hash,(gpointer)kmer,poi); ^ kmer_glib_index.dy: In function 'Wise2_retrieve_active_kmer_KmerGlibIndex': kmer_glib_index.dy:124:40: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] kgi->active_index[kgi->kmer_pos++] = (kmer_t) key; ^ cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models singleseqspace.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models dnamapping.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models largeseqreader.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_untangler.c kmer_assembly_untangler.dy: In function 'Wise2_untangle_KmerAssembly': kmer_assembly_untangler.dy:120:7: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t' [-Wformat=] fprintf(stderr,"TANGLE: Node %ld, %s has forward %d and back %d links\n",node->number,buffer,node->next_len,node->prev_len); ^ kmer_assembly_untangler.dy:141:7: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t' [-Wformat=] fprintf(stderr,"Will attempt untangle starting at %ld to %ld\n",node->prev[i]->prev->number,node->number); ^ kmer_assembly_untangler.dy:141:7: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'kmer_t' [-Wformat=] kmer_assembly_untangler.dy:157:7: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t' [-Wformat=] fprintf(stderr,"RESOLVED: Node %ld [%s] Fully untangled now...\n",node->number,buffer); ^ kmer_assembly_untangler.dy:159:7: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t' [-Wformat=] fprintf(stderr,"UNRESOLVED: Node %ld [%s] still tangled...\n",node->number,buffer); ^ kmer_assembly_untangler.dy: In function 'Wise2_old_attempt_forward_untangle_KmerAssembly': kmer_assembly_untangler.dy:444:5: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t' [-Wformat=] fprintf(stderr,"looking at node %ld with path length %d, next length %d depth %d\n",current->next->number,pathlen,current->next->next_len,current->sequence_label_len); ^ kmer_assembly_untangler.dy:568:2: warning: passing argument 4 of 'Wise2_lift_backward_tangled_tail' from incompatible pointer type [enabled by default] lift_backward_tangled_tail(kai,newpath->stack[newpath->stack_len-1],path,transferred_label,transferred_pos,transferred_len); ^ In file included from kmer_assembly_untangler.c:4:0: kmer_assembly_untangler.h:174:6: note: expected 'int *' but argument is of type 'long int *' void Wise2_lift_backward_tangled_tail(KmerAssemblyIndex * kai,KmerAssemblyLink * new,KmerAssemblyPath * tail,int * start_label,SinglePosSequence ** positions,int label_len); ^ kmer_assembly_untangler.dy: In function 'Wise2_lift_forward_tangled_KmerAssemblyPath': kmer_assembly_untangler.dy:746:5: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'kmer_t' [-Wformat=] fprintf(stderr,"Moving stack position %d, depth %d, transfer %d, between %ld [%s] and %ld [%s]\n",i,kap->stack[i]->sequence_label_len,label_len,kap->stack[i]->prev->number,back,kap->stack[i]->next->number,forw); ^ kmer_assembly_untangler.dy:746:5: warning: format '%ld' expects argument of type 'long int', but argument 8 has type 'kmer_t' [-Wformat=] cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_contig.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_error.c kmer_assembly_error.dy: In function 'Wise2_mark_tangles_KmerAssembly': kmer_assembly_error.dy:93:7: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t' [-Wformat=] fprintf(stderr,"Marking node (%ld) [%s] as next tangled\n",node->number,buffer); ^ kmer_assembly_error.dy:105:7: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'kmer_t' [-Wformat=] fprintf(stderr,"Marking node (%ld) [%s] as prev tangled\n",node->number,buffer); ^ kmer_assembly_error.dy: In function 'Wise2_extend_indel_path_KmerAssembly': kmer_assembly_error.dy:351:2: warning: format '%d' expects argument of type 'int', but argument 4 has type 'int *' [-Wformat=] fprintf(stderr,"in considering indel (%d, path %d), real (%c) and error (%c) do not agree at position %d,%d\n",delete_length,current_path,real->base,error->base,real_pos,error_pos); ^ cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models compressed_protein_index.c compressed_protein_index.dy: In function 'Wise2_add_direct_number_CompressedProteinIndex': compressed_protein_index.dy:223:3: warning: return makes integer from pointer without a cast [enabled by default] return NULL; ^ make[3]: Leaving directory `/build/buildd/wise-2.4.1/src/dnaindex' (cd network ; /usr/bin/make CC="cc" CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c `pkg-config --cflags glib-2.0`" all ) make[3]: Entering directory `/build/buildd/wise-2.4.1/src/network' cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex wise_proteinindex_server.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex net_hspscan.c cc -g -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -ldyna_glib -ldyna -lwisesocket -lwisebase -Wl,-Bsymbolic-functions -Wl,-z,relro -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config --libs glib-2.0` -lpthread cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex client_multihspscan.c make[3]: Leaving directory `/build/buildd/wise-2.4.1/src/network' (cd models ; /usr/bin/make CC="cc" CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c `pkg-config --cflags glib-2.0`" EXTRALIBS="-lm" HMMER_DEFINE="HMMER_INTERNAL" HMMER_INCLUDE="../HMMer2/" HMMER_LIBS="../HMMer2/" all ) make[3]: Entering directory `/build/buildd/wise-2.4.1/src/models' cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dnal.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dnaalign.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ seqaligndisplay.c cc -o dnal dnal.o dnaalign.o seqaligndisplay.o -Wl,-Bsymbolic-functions -Wl,-z,relro -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ psw.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ proteinsw.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ sw_wrap.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ abc.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pba.c cc -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -Wl,-Bsymbolic-functions -Wl,-z,relro -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pswdb.c cc -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -Wl,-Bsymbolic-functions -Wl,-z,relro -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dbac.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dba.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ slimdba.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ bigdba.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dbadisplay.c cc -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o -Wl,-Bsymbolic-functions -Wl,-z,relro -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include estwise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparser21.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparameter.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genestats.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisehsp.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneutil.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneoutput.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ threestatemodel.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genefrequency.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ splicesitemodeler.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise4.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise6.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genestretch6.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise21.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneloop21.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneloop6.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genephase6.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ gwlite.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ gwlitemodel.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ gwrap.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ matchsum.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estwrap.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisemodel.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ phasemodel.c phasemodel.dy: In function 'Wise2_read_fasta_PhasedProtein': phasemodel.dy:241:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(name,10000,ifp); ^ In file included from /usr/include/stdio.h:937:0, from ../base/wisebase.h:6, from ../dynlibsrc/probability.h:7, from geneparser21.h:6, from genewisemodel.h:6, from phasemodel.h:6, from phasemodel.c:4: In function 'fgets', inlined from 'Wise2_read_fasta_PhasedProtein' at phasemodel.dy:241:8: /usr/include/i386-linux-gnu/bits/stdio2.h:261:2: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [enabled by default] return __fgets_chk_warn (__s, __bos (__s), __n, __stream); ^ cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ cdparser.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genedisplay.c genedisplay.dy: In function 'Wise2_write_intron_desc': genedisplay.dy:493:5: warning: too many arguments for format [-Wformat-extra-args] sprintf(buffer," Intron ??? ",in_number); ^ cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estwise3.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estslim3.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estloop3.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estfrag3.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estslimloop.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ gwquickdb.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ threestatedb.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pfamhmmer1db.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pwmdna.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../HMMer2/ -DHMMER_INTERNAL -I../base/ -I../dynlibsrc/ wise2xhmmer2.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisemodeldb.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ seqhit.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ standardout.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparser4.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estquick3.c cc -g -o estwise estwise.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-Bsymbolic-functions -Wl,-z,relro -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -Wl,-Bsymbolic-functions -Wl,-z,relro -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include genewise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. cc -o genewise genewise.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-Bsymbolic-functions -Wl,-z,relro -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm -Wl,-Bsymbolic-functions -Wl,-z,relro -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include genewisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ cc -g -o genewisedb genewisedb.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-Bsymbolic-functions -Wl,-z,relro -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -Wl,-Bsymbolic-functions -Wl,-z,relro -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include estwisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ cc -g -o estwisedb estwisedb.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-Bsymbolic-functions -Wl,-z,relro -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -Wl,-Bsymbolic-functions -Wl,-z,relro -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genomewise.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genomewise9.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genome_evidence.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ est_evidence.c est_evidence.dy: In function 'Wise2_new_est_GenomeEvidenceUnit': est_evidence.dy:142:16: warning: assignment from incompatible pointer type [enabled by default] in->geu_free = free_EstEvidence; ^ cc -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o -Wl,-Bsymbolic-functions -Wl,-z,relro -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ sywise.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ sywise20.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ syexonmodel.c cc -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o -Wl,-Bsymbolic-functions -Wl,-z,relro -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pseudowise.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pseudowise7.c cc -g -o pseudowise pseudowise.o pseudowise7.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-Bsymbolic-functions -Wl,-z,relro -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -Wl,-Bsymbolic-functions -Wl,-z,relro -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` promoterwise.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ localdba.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` localcishit.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ localcispara.c cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/i386-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ motifmatrix.c motifmatrix.c: In function 'Wise2_MotifConsMatrix_alloc_matrix': motifmatrix.c:408:24: warning: assignment makes integer from pointer without a cast [enabled by default] for(i=0;i dba.1 docbook-to-man dnal.sgml > dnal.1 docbook-to-man estwise.sgml > estwise.1 docbook-to-man estwisedb.sgml > estwisedb.1 docbook-to-man genewise.sgml > genewise.1 docbook-to-man genewisedb.sgml > genewisedb.1 docbook-to-man genomewise.sgml > genomewise.1 docbook-to-man promoterwise.sgml > promoterwise.1 docbook-to-man psw.sgml > psw.1 docbook-to-man pswdb.sgml > pswdb.1 docbook-to-man scanwise.sgml > scanwise.1 docbook-to-man scanwise_server.sgml > scanwise_server.1 make[2]: Leaving directory `/build/buildd/wise-2.4.1/debian/manpages.d' cat src/models/*.tex src/dynlibsrc/*.tex | perl docs/gettex.pl > docs/temp.tex cat docs/wise2api.tex docs/temp.tex docs/apiend.tex > docs/api.tex sed -i 's/ sw_wrap / sw\\_wrap /' docs/api.tex sed -i 's/label{module_sequence\\_codon}/label{module_sequence_codon}/' docs/api.tex sed -i 's/Wise2::GeneParameter21_wrap/Wise2::GeneParameter21\\_wrap/' docs/api.tex cd docs && pdflatex api.tex This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013/Debian) restricted \write18 enabled. entering extended mode (./api.tex LaTeX2e <2011/06/27> Babel <3.9f> and hyphenation patterns for 2 languages loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/latex209.def Entering LaTeX 2.09 COMPATIBILITY MODE ************************************************************* !!WARNING!! !!WARNING!! !!WARNING!! !!WARNING!! This mode attempts to provide an emulation of the LaTeX 2.09 author environment so that OLD documents can be successfully processed. It should NOT be used for NEW documents! New documents should use Standard LaTeX conventions and start with the \documentclass command. Compatibility mode is UNLIKELY TO WORK with LaTeX 2.09 style files that change any internal macros, especially not with those that change the FONT SELECTION or OUTPUT ROUTINES. Therefore such style files MUST BE UPDATED to use Current Standard LaTeX: LaTeX2e. If you suspect that you may be using such a style file, which is probably very, very old by now, then you should attempt to get it updated by sending a copy of this error message to the author of that file. ************************************************************* (/usr/share/texlive/texmf-dist/tex/latex/base/tracefnt.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/latexsym.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) No file api.aux. (/usr/share/texlive/texmf-dist/tex/latex/base/ulasy.fd) [1{/var/lib/texmf/fonts /map/pdftex/updmap/pdftex.map}] No file api.toc. [2] [3] Overfull \hbox (1.49698pt too wide) in paragraph at lines 107--107 [] \OT1/cmtt/m/n/10 print "You must give a file to revcom for a reverse to w ork!";[] [4] [5] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) LaTeX Warning: Reference `object_CodonTable' on page 6 undefined on input line 196. LaTeX Warning: Reference `object_Sequence' on page 6 undefined on input line 19 7. LaTeX Warning: Reference `object_CompMat' on page 6 undefined on input line 203 . LaTeX Warning: Reference `object_Sequence' on page 6 undefined on input line 20 4. LaTeX Warning: Reference `object_Protein' on page 6 undefined on input line 205 . LaTeX Warning: Reference `object_CompMat' on page 6 undefined on input line 206 . LaTeX Warning: Reference `module_sw_wrap' on page 6 undefined on input line 207 . LaTeX Warning: Reference `module_seqaligndisplay' on page 6 undefined on input line 208. LaTeX Warning: Reference `object_Protein' on page 6 undefined on input line 213 . LaTeX Warning: Reference `object_Sequence' on page 6 undefined on input line 21 3. [6] LaTeX Warning: Reference `object_ProteinDB' on page 7 undefined on input line 2 14. LaTeX Warning: Reference `object_ProteinDB' on page 7 undefined on input line 2 15. LaTeX Warning: Reference `module_sw_wrap' on page 7 undefined on input line 216 . LaTeX Warning: Reference `object_Hscore' on page 7 undefined on input line 217. LaTeX Warning: Reference `object_DataEntry' on page 7 undefined on input line 2 19. LaTeX Warning: Reference `object_ProteinDB' on page 7 undefined on input line 2 19. LaTeX Warning: Reference `object_Sequence' on page 7 undefined on input line 22 6. LaTeX Warning: Reference `object_Protein' on page 7 undefined on input line 227 . LaTeX Warning: Reference `object_Sequence' on page 7 undefined on input line 22 8. LaTeX Warning: Reference `object_Genomic' on page 7 undefined on input line 229 . LaTeX Warning: Reference `object_GeneFrequency' on page 7 undefined on input li ne 231. LaTeX Warning: Reference `object_CodonTable' on page 7 undefined on input line 232. LaTeX Warning: Reference `object_RandomModelDNA' on page 7 undefined on input l ine 233. LaTeX Warning: Reference `module_gwrap' on page 7 undefined on input line 234. LaTeX Warning: Reference `module_gwrap' on page 7 undefined on input line 235. Overfull \hbox (21.30891pt too wide) in paragraph at lines 235--236 []\OT1/cmr/m/n/10 Build an en-tire pa-ram-e-ter set for ge-newise us-ing Wise2: :GeneParameter21[]wrap LaTeX Warning: Reference `module_gwrap' on page 7 undefined on input line 236. LaTeX Warning: Reference `module_gwrap' on page 7 undefined on input line 237. [7] [8] [9] LaTeX Warning: Reference `module_gwrap' on page 10 undefined on input line 387. [10] LaTeX Warning: Reference `module_estwrap' on page 11 undefined on input line 38 9. LaTeX Warning: Reference `module_sw_wrap' on page 11 undefined on input line 39 1. LaTeX Warning: Reference `module_genedisplay' on page 11 undefined on input lin e 393. LaTeX Warning: Reference `module_seqaligndisplay' on page 11 undefined on input line 395. LaTeX Warning: Reference `module_threestatemodel' on page 11 undefined on input line 397. LaTeX Warning: Reference `module_threestatedb' on page 11 undefined on input li ne 398. LaTeX Warning: Reference `module_genefrequency' on page 11 undefined on input l ine 399. LaTeX Warning: Reference `module_geneparameter' on page 11 undefined on input l ine 400. LaTeX Warning: Reference `module_cdparser' on page 11 undefined on input line 4 01. LaTeX Warning: Reference `module_sequence' on page 11 undefined on input line 4 08. LaTeX Warning: Reference `module_sequencedb' on page 11 undefined on input line 409. LaTeX Warning: Reference `module_protein' on page 11 undefined on input line 41 0. LaTeX Warning: Reference `module_proteindb' on page 11 undefined on input line 411. LaTeX Warning: Reference `module_genomic' on page 11 undefined on input line 41 2. LaTeX Warning: Reference `module_genomicdb' on page 11 undefined on input line 413. LaTeX Warning: Reference `module_cdna' on page 11 undefined on input line 414. LaTeX Warning: Reference `module_cdnadb' on page 11 undefined on input line 415 . LaTeX Warning: Reference `module_probability' on page 11 undefined on input lin e 421. LaTeX Warning: Reference `module_codon' on page 11 undefined on input line 422. LaTeX Warning: Reference `module_compmat' on page 11 undefined on input line 42 3. LaTeX Warning: Reference `module_codonmat' on page 11 undefined on input line 4 24. LaTeX Warning: Reference `module_codonmapper' on page 11 undefined on input lin e 425. [11] LaTeX Warning: Reference `module_hscore' on page 12 undefined on input line 431 . LaTeX Warning: Reference `module_histogram' on page 12 undefined on input line 432. LaTeX Warning: Reference `module_dbimpl' on page 12 undefined on input line 433 . LaTeX Warning: Reference `module_aln' on page 12 undefined on input line 439. LaTeX Warning: Reference `module_packaln' on page 12 undefined on input line 44 0. LaTeX Warning: Reference `module_basematrix' on page 12 undefined on input line 441. LaTeX Warning: Reference `object_cDNAParser' on page 12 undefined on input line 449. LaTeX Warning: Reference `accessing_fields' on page 12 undefined on input line 479. [12] LaTeX Warning: Reference `object_DnaStartEnd' on page 13 undefined on input lin e 502. Overfull \hbox (62.7533pt too wide) in paragraph at lines 509--510 []\OT1/cmtt/m/n/10 Wise2[]make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap, text,dpri) Overfull \hbox (40.0498pt too wide) in paragraph at lines 510--511 []\OT1/cmtt/m/n/10 &Wise2::make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap ,text,dpri) [13] LaTeX Warning: Reference `accessing_fields' on page 14 undefined on input line 555. Overfull \hbox (335.96082pt too wide) in paragraph at lines 571--572 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]TSM[]estwise (tdb,cdb,cp,cm,rmd,use[]sy n,alg,bits[]cutoff,allN,flat[]insert,report[]level,die[]on[]error,dbsi) Overfull \hbox (313.25732pt too wide) in paragraph at lines 572--573 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]TSM[]estwise (tdb,cdb,cp,cm,rmd,use[]s yn,alg,bits[]cutoff,allN,flat[]insert,report[]level,die[]on[]error,dbsi) [14] Overfull \hbox (329.87091pt too wide) in paragraph at lines 598--599 []\OT1/cmtt/m/n/10 Wise2[]AlnBlock[]from[]Protein[]estwise[]wrap (pro,cdna,cp,c m,ct,comp,gap,ext,is[]global,rmd,alg,rm,use[]syn,allN,dpri,palpoi) Overfull \hbox (270.41774pt too wide) in paragraph at lines 599--600 []\OT1/cmtt/m/n/10 &Wise2::AlnBlock[]from[]Protein[]estwise[]wrap (pro,cdna,cp, cm,ct,comp,gap,ext,is[]global,rmd,alg,rm,use[]syn,allN,dpri) [15] Overfull \hbox (265.40146pt too wide) in paragraph at lines 632--633 []\OT1/cmtt/m/n/10 Wise2[]AlnBlock[]from[]TSM[]estwise[]wrap (tsm,cdna,cp,cm,ct ,rmd,alg,use[]syn,force[]flat[]insert,allN,dpri,palpoi) Overfull \hbox (205.94829pt too wide) in paragraph at lines 633--634 []\OT1/cmtt/m/n/10 &Wise2::AlnBlock[]from[]TSM[]estwise[]wrap (tsm,cdna,cp,cm,c t,rmd,alg,use[]syn,force[]flat[]insert,allN,dpri) [16] Overfull \hbox (47.00343pt too wide) in paragraph at lines 680--681 []\OT1/cmtt/m/n/10 Wise2[]protein2genomic[]ascii[]display (alb,p,gen,ct,name,ma in,ofp) Overfull \hbox (24.29994pt too wide) in paragraph at lines 681--682 []\OT1/cmtt/m/n/10 &Wise2::protein2genomic[]ascii[]display (alb,p,gen,ct,name,m ain,ofp) Overfull \hbox (188.7522pt too wide) in paragraph at lines 701--702 []\OT1/cmtt/m/n/10 Wise2[]protcdna[]ascii[]display (alb,protsequence,protname,p rotoff,cdna,ct,name,main,mult,ofp) Overfull \hbox (166.0487pt too wide) in paragraph at lines 702--703 []\OT1/cmtt/m/n/10 &Wise2::protcdna[]ascii[]display (alb,protsequence,protname, protoff,cdna,ct,name,main,mult,ofp) [17] LaTeX Warning: Reference `object_GeneFrequency21' on page 18 undefined on input line 730. LaTeX Warning: Reference `object_GeneConsensus' on page 18 undefined on input l ine 732. LaTeX Warning: Reference `object_GeneSingleCons' on page 18 undefined on input line 734. [18] LaTeX Warning: Reference `accessing_fields' on page 19 undefined on input line 779. Overfull \hbox (1.40793pt too wide) in paragraph at lines 793--794 []\OT1/cmr/m/n/10 transition[GENEFREQUENCY21[]TRANSITION[]LEN] Type [dou-ble : Scalar] LaTeX Warning: Reference `accessing_fields' on page 19 undefined on input line 806. [19] LaTeX Warning: Reference `accessing_fields' on page 20 undefined on input line 821. LaTeX Warning: Reference `object_GeneParameter21' on page 20 undefined on input line 837. LaTeX Warning: Reference `accessing_fields' on page 20 undefined on input line 844. [20] LaTeX Warning: Reference `object_MatchSummarySet' on page 21 undefined on input line 890. LaTeX Warning: Reference `object_MatchSummary' on page 21 undefined on input li ne 892. LaTeX Warning: Reference `accessing_fields' on page 21 undefined on input line 899. Overfull \hbox (71.7832pt too wide) in paragraph at lines 914--915 []\OT1/cmtt/m/n/10 Wise2[]MatchSummarySet[]from[]AlnBlock[]estwise (alb,qname,o ffset,target) Overfull \hbox (1.83012pt too wide) in paragraph at lines 915--916 []\OT1/cmtt/m/n/10 &Wise2::MatchSummarySet::MatchSummarySet[]from[]AlnBlock[]es twise Overfull \hbox (62.22557pt too wide) in paragraph at lines 917--918 []\OT1/cmtt/m/n/10 $obj->MatchSummarySet[]from[]AlnBlock[]estwise(qname,offset, target) [21] Overfull \hbox (82.28311pt too wide) in paragraph at lines 940--941 []\OT1/cmtt/m/n/10 Wise2[]MatchSummarySet[]from[]AlnBlock[]genewise (alb,qname, protoff,target) Overfull \hbox (7.08008pt too wide) in paragraph at lines 941--942 []\OT1/cmtt/m/n/10 &Wise2::MatchSummarySet::MatchSummarySet[]from[]AlnBlock[]ge newise Overfull \hbox (72.72548pt too wide) in paragraph at lines 943--944 []\OT1/cmtt/m/n/10 $obj->MatchSummarySet[]from[]AlnBlock[]genewise(qname,protof f,target) LaTeX Warning: Reference `accessing_fields' on page 22 undefined on input line 965. [22] LaTeX Warning: Reference `object_PfamHmmer1DB' on page 23 undefined on input li ne 1007. LaTeX Warning: Reference `object_PfamHmmer1Entry' on page 23 undefined on input line 1009. LaTeX Warning: Reference `accessing_fields' on page 23 undefined on input line 1016. LaTeX Warning: Reference `accessing_fields' on page 23 undefined on input line 1052. [23] Overfull \hbox (92.78302pt too wide) in paragraph at lines 1074--1075 []\OT1/cmtt/m/n/10 Wise2[]write[]pretty[]str[]align (alb,qname,query,tname,targ et,name,main,ofp) Overfull \hbox (70.07953pt too wide) in paragraph at lines 1075--1076 []\OT1/cmtt/m/n/10 &Wise2::write[]pretty[]str[]align (alb,qname,query,tname,tar get,name,main,ofp) [24] Overfull \hbox (3.5338pt too wide) in paragraph at lines 1117--1118 []\OT1/cmtt/m/n/10 Wise2[]write[]pretty[]Protein[]align (alb,q,t,name,main,ofp) LaTeX Warning: Reference `object_DnaSequenceHitList' on page 25 undefined on in put line 1143. LaTeX Warning: Reference `object_SegmentHitList' on page 25 undefined on input line 1145. LaTeX Warning: Reference `object_SegmentHit' on page 25 undefined on input line 1147. [25] LaTeX Warning: Reference `accessing_fields' on page 26 undefined on input line 1154. Overfull \hbox (29.5499pt too wide) in paragraph at lines 1190--1191 []\OT1/cmtt/m/n/10 &Wise2::DnaSequenceHitList::read[]MSPcrunch[]DnaSequenceHitL ist (ifp) [26] LaTeX Warning: Reference `accessing_fields' on page 27 undefined on input line 1207. LaTeX Warning: Reference `accessing_fields' on page 27 undefined on input line 1220. Overfull \hbox (99.50298pt too wide) in paragraph at lines 1248--1249 []\OT1/cmtt/m/n/10 Wise2[]Align[]strings[]ProteinSmithWaterman (one,two,comp,ga p,ext,dpenv,dpri) Overfull \hbox (76.79948pt too wide) in paragraph at lines 1249--1250 []\OT1/cmtt/m/n/10 &Wise2::Align[]strings[]ProteinSmithWaterman (one,two,comp,g ap,ext,dpenv,dpri) [27] Overfull \hbox (110.00288pt too wide) in paragraph at lines 1273--1274 []\OT1/cmtt/m/n/10 Wise2[]Align[]Sequences[]ProteinSmithWaterman (one,two,comp, gap,ext,dpenv,dpri) Overfull \hbox (87.2994pt too wide) in paragraph at lines 1274--1275 []\OT1/cmtt/m/n/10 &Wise2::Align[]Sequences[]ProteinSmithWaterman (one,two,comp ,gap,ext,dpenv,dpri) Overfull \hbox (7.58401pt too wide) in paragraph at lines 1286--1287 []\OT1/cmr/m/n/10 [OWNER] new AlnBlock struc-ture rep-re-sent-ing the align-men t [AlnBlock [28] Overfull \hbox (68.00325pt too wide) in paragraph at lines 1307--1308 []\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]SmithWaterman (one,two,comp,gap,ext, dpenv,dpri) Overfull \hbox (45.29976pt too wide) in paragraph at lines 1308--1309 []\OT1/cmtt/m/n/10 &Wise2::Align[]Proteins[]SmithWaterman (one,two,comp,gap,ext ,dpenv,dpri) Overfull \hbox (5.0038pt too wide) in paragraph at lines 1334--1335 []\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]ABC (one,two,comp,a,b,c,dpenv,dpri) [29] Overfull \hbox (47.00343pt too wide) in paragraph at lines 1355--1356 []\OT1/cmtt/m/n/10 Wise2[]Align[]Sequences[]ProteinABC (one,two,comp,a,b,c,dpen v,dpri) Overfull \hbox (24.29994pt too wide) in paragraph at lines 1356--1357 []\OT1/cmtt/m/n/10 &Wise2::Align[]Sequences[]ProteinABC (one,two,comp,a,b,c,dpe nv,dpri) Overfull \hbox (86.01088pt too wide) in paragraph at lines 1371--1374 \OT1/cmr/m/n/10 Align[]Sequences[]ProteinABC this func-tion is anal-o-gous to A lign[]Sequences[]ProteinSmithWaterman Overfull \hbox (240.62169pt too wide) in paragraph at lines 1378--1379 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinSW (querydb,targetdb,comp,gap,ex t,bits[]cutoff,report[]level,die[]on[]error,dbsi) Overfull \hbox (217.9182pt too wide) in paragraph at lines 1379--1380 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinSW (querydb,targetdb,comp,gap,e xt,bits[]cutoff,report[]level,die[]on[]error,dbsi) [30] Overfull \hbox (235.37173pt too wide) in paragraph at lines 1400--1401 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b,c ,bits[]cutoff,report[]level,die[]on[]error,dbsi) Overfull \hbox (212.66824pt too wide) in paragraph at lines 1401--1402 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b, c,bits[]cutoff,report[]level,die[]on[]error,dbsi) [31] Overfull \hbox (359.90063pt too wide) in paragraph at lines 1423--1424 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinBA (querydb,targetdb,comp,bentry ,bexit,bfor[]trans,b[]self[]trans,b3exit,bits[]cutoff,report[]level,dbsi) Overfull \hbox (337.19714pt too wide) in paragraph at lines 1424--1425 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinBA (querydb,targetdb,comp,bentr y,bexit,bfor[]trans,b[]self[]trans,b3exit,bits[]cutoff,report[]level,dbsi) LaTeX Warning: Reference `object_ThreeStateDB' on page 32 undefined on input li ne 1452. LaTeX Warning: Reference `accessing_fields' on page 32 undefined on input line 1459. [32] Overfull \hbox (15.42177pt too wide) in paragraph at lines 1487--1488 []\OT1/cmr/m/n/10 reload[]generic Type [Three-State-Model * (*reload[]generic)( ThreeStateDB * tdb,int Overfull \hbox (3.42192pt too wide) in paragraph at lines 1494--1495 []\OT1/cmr/m/n/10 dataentry[]add Type [boolean (*dataen-try[]add)(ThreeStateDB * tdb,DataEntry Overfull \hbox (41.78299pt too wide) in paragraph at lines 1498--1499 []\OT1/cmr/m/n/10 index[]generic Type [Three-State-Model * (*in-dex[]generic)(T hreeStateDB *tdb,DataEntry [33] Overfull \hbox (29.5499pt too wide) in paragraph at lines 1569--1570 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateDB::new[]proteindb[]ThreeStateDB (sdb,comp ,gap,ext) [34] [35] LaTeX Warning: Reference `object_ThreeStateModel' on page 36 undefined on input line 1632. LaTeX Warning: Reference `object_ThreeStateUnit' on page 36 undefined on input line 1634. LaTeX Warning: Reference `accessing_fields' on page 36 undefined on input line 1675. [36] Overfull \hbox (16.10999pt too wide) in paragraph at lines 1702--1703 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::force[]global[]model (tsm,prob[]int o[]model) Overfull \hbox (102.65288pt too wide) in paragraph at lines 1722--1723 []\OT1/cmtt/m/n/10 Wise2[]force[]weighted[]local[]model (tsm,prob[]into[]model, ratio[]start,ratio[]end) Overfull \hbox (169.19861pt too wide) in paragraph at lines 1723--1724 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::force[]weighted[]local[]model (tsm, prob[]into[]model,ratio[]start,ratio[]end) Overfull \hbox (93.09525pt too wide) in paragraph at lines 1725--1726 []\OT1/cmtt/m/n/10 $obj->force[]weighted[]local[]model(prob[]into[]model,ratio[ ]start,ratio[]end) Overfull \hbox (49.31339pt too wide) in paragraph at lines 1745--1746 []\OT1/cmtt/m/n/10 Wise2[]ThreeStateModel[]from[]half[]bit[]Sequence (pro,mat,r m,gap,ext) [37] Overfull \hbox (5.61008pt too wide) in paragraph at lines 1746--1747 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::ThreeStateModel[]from[]half[]bit[]S equence Overfull \hbox (39.75575pt too wide) in paragraph at lines 1748--1749 []\OT1/cmtt/m/n/10 $obj->ThreeStateModel[]from[]half[]bit[]Sequence(mat,rm,gap, ext) Overfull \hbox (51.38966pt too wide) in paragraph at lines 1772--1773 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::write[]HMMer[]1[]7[]ascii[]ThreeSta teModel (tsm,ofp) LaTeX Warning: Reference `accessing_fields' on page 38 undefined on input line 1790. [38] LaTeX Warning: Reference `object_AlnBlock' on page 39 undefined on input line 1 815. LaTeX Warning: Reference `object_AlnColumn' on page 39 undefined on input line 1817. LaTeX Warning: Reference `object_AlnUnit' on page 39 undefined on input line 18 19. LaTeX Warning: Reference `object_AlnSequence' on page 39 undefined on input lin e 1821. LaTeX Warning: Reference `accessing_fields' on page 39 undefined on input line 1828. Overfull \hbox (6.8248pt too wide) in paragraph at lines 1839--1846 \OT1/cmr/m/n/10 AlnBlock is the main rep-re-sen-ta-tion of align-ments from Dy- na-mite. Each AlnBlock [39] LaTeX Warning: Reference `accessing_fields' on page 40 undefined on input line 1877. LaTeX Warning: Reference `accessing_fields' on page 40 undefined on input line 1919. [40] [41] LaTeX Warning: Reference `accessing_fields' on page 42 undefined on input line 1987. LaTeX Warning: Reference `object_AlnRange' on page 42 undefined on input line 2 016. LaTeX Warning: Reference `object_AlnRangeSet' on page 42 undefined on input lin e 2018. LaTeX Warning: Reference `accessing_fields' on page 42 undefined on input line 2025. [42] LaTeX Warning: Reference `accessing_fields' on page 43 undefined on input line 2052. [43] LaTeX Warning: Reference `object_cDNA' on page 44 undefined on input line 2105. LaTeX Warning: Reference `accessing_fields' on page 44 undefined on input line 2112. [44] [45] LaTeX Warning: Reference `object_cDNADB' on page 46 undefined on input line 224 8. [46] LaTeX Warning: Reference `accessing_fields' on page 47 undefined on input line 2288. [47] LaTeX Warning: Reference `object_CodonTable' on page 48 undefined on input line 2369. [48] [49] [50] [51] LaTeX Warning: Reference `accessing_fields' on page 52 undefined on input line 2577. [52] [53] [54] LaTeX Warning: Reference `object_CodonMapper' on page 55 undefined on input lin e 2727. LaTeX Warning: Reference `accessing_fields' on page 55 undefined on input line 2755. [55] Overfull \hbox (12.33003pt too wide) in paragraph at lines 2782--2783 []\OT1/cmtt/m/n/10 &Wise2::CodonMapper::sprinkle[]errors[]over[]CodonMapper (cm ,error) LaTeX Warning: Reference `object_ComplexSequence' on page 56 undefined on input line 2806. LaTeX Warning: Reference `object_ComplexSequenceEvalSet' on page 56 undefined o n input line 2808. LaTeX Warning: Reference `accessing_fields' on page 56 undefined on input line 2815. [56] LaTeX Warning: Reference `accessing_fields' on page 57 undefined on input line 2846. LaTeX Warning: Reference `object_CompMat' on page 57 undefined on input line 28 81. LaTeX Warning: Reference `accessing_fields' on page 57 undefined on input line 2888. [57] [58] LaTeX Warning: Reference `object_DBSearchImpl' on page 59 undefined on input li ne 2988. [59] LaTeX Warning: Reference `accessing_fields' on page 60 undefined on input line 3035. [60] LaTeX Warning: Reference `object_DnaMatrix' on page 61 undefined on input line 3100. LaTeX Warning: Reference `object_DnaProbMatrix' on page 61 undefined on input l ine 3102. [61] LaTeX Warning: Reference `accessing_fields' on page 62 undefined on input line 3163. LaTeX Warning: Reference `accessing_fields' on page 62 undefined on input line 3176. [62] LaTeX Warning: Reference `object_Gene' on page 63 undefined on input line 3208. LaTeX Warning: Reference `accessing_fields' on page 63 undefined on input line 3215. [63] [64] LaTeX Warning: Reference `object_Genomic' on page 65 undefined on input line 33 12. LaTeX Warning: Reference `object_GenomicRepeat' on page 65 undefined on input l ine 3314. [65] Overfull \hbox (0.5938pt too wide) in paragraph at lines 3353--3354 []\OT1/cmtt/m/n/10 Wise2[]Genomic[]from[]Sequence[]Nheuristic (seq,length[]of[] N) LaTeX Warning: Reference `accessing_fields' on page 66 undefined on input line 3402. [66] [67] LaTeX Warning: Reference `accessing_fields' on page 68 undefined on input line 3514. [68] LaTeX Warning: Reference `object_GenomicDB' on page 69 undefined on input line 3532. Overfull \hbox (65.9032pt too wide) in paragraph at lines 3539--3540 []\OT1/cmtt/m/n/10 Wise2[]new[]GenomicDB[]from[]single[]seq (gen,cses,score[]in []repeat[]coding) Overfull \hbox (43.1997pt too wide) in paragraph at lines 3540--3541 []\OT1/cmtt/m/n/10 &Wise2::new[]GenomicDB[]from[]single[]seq (gen,cses,score[]i n[]repeat[]coding) Overfull \hbox (41.12343pt too wide) in paragraph at lines 3556--3557 []\OT1/cmtt/m/n/10 Wise2[]new[]GenomicDB (seqdb,cses,length[]of[]N,repeat[]in[] cds[]score) Overfull \hbox (18.41994pt too wide) in paragraph at lines 3557--3558 []\OT1/cmtt/m/n/10 &Wise2::new[]GenomicDB (seqdb,cses,length[]of[]N,repeat[]in[ ]cds[]score) [69] LaTeX Warning: Reference `accessing_fields' on page 70 undefined on input line 3577. [70] LaTeX Warning: Reference `object_GenomicRegion' on page 71 undefined on input l ine 3662. LaTeX Warning: Reference `accessing_fields' on page 71 undefined on input line 3669. [71] Overfull \hbox (1.83012pt too wide) in paragraph at lines 3712--3713 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::read[]EMBL[]GenomicRegion[]file (file name) [72] Overfull \hbox (7.08008pt too wide) in paragraph at lines 3765--3766 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::show[]ace[]GenomicRegion (gr,seq[]nam e,ofp) Overfull \hbox (3.5338pt too wide) in paragraph at lines 3790--3791 []\OT1/cmtt/m/n/10 Wise2[]show[]pretty[]GenomicRegion (gr,show[]supporting,ofp) Overfull \hbox (59.57962pt too wide) in paragraph at lines 3791--3792 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::show[]pretty[]GenomicRegion (gr,show[ ]supporting,ofp) [73] [74] LaTeX Warning: Reference `object_Histogram' on page 75 undefined on input line 3869. [75] LaTeX Warning: Reference `accessing_fields' on page 76 undefined on input line 3917. Overfull \hbox (32.9967pt too wide) in paragraph at lines 3956--3956 [] \OT1/cmtt/m/n/10 b) cooperation with future versions of histogram.c would be possible.[] [76] [77] [78] Overfull \hbox (123.4428pt too wide) in paragraph at lines 4158--4159 []\OT1/cmtt/m/n/10 Wise2[]ExtremeValueSetHistogram (h,mu,lambda,lowbound,highbo und,wonka,ndegrees) Overfull \hbox (67.76958pt too wide) in paragraph at lines 4159--4160 []\OT1/cmtt/m/n/10 &Wise2::Histogram::set[]EVD (h,mu,lambda,lowbound,highbound, wonka,ndegrees) Overfull \hbox (33.66585pt too wide) in paragraph at lines 4161--4162 []\OT1/cmtt/m/n/10 $obj->set[]EVD(mu,lambda,lowbound,highbound,wonka,ndegrees) [79] [80] [81] LaTeX Warning: Reference `object_Hscore' on page 82 undefined on input line 429 4. LaTeX Warning: Reference `object_DataScore' on page 82 undefined on input line 4296. LaTeX Warning: Reference `object_DataEntry' on page 82 undefined on input line 4298. LaTeX Warning: Reference `accessing_fields' on page 82 undefined on input line 4325. Overfull \hbox (30.97293pt too wide) in paragraph at lines 4335--4336 []\OT1/cmr/m/n/10 should[]store Type [boolean (*should[]store)(int given[]score ,double in-ter-nal[]score[]level) [82] [83] [84] LaTeX Warning: Reference `accessing_fields' on page 85 undefined on input line 4526. [85] LaTeX Warning: Reference `accessing_fields' on page 86 undefined on input line 4552. LaTeX Warning: Reference `object_PackAln' on page 86 undefined on input line 45 93. [86] LaTeX Warning: Reference `object_PackAlnUnit' on page 87 undefined on input lin e 4595. LaTeX Warning: Reference `accessing_fields' on page 87 undefined on input line 4602. [87] LaTeX Warning: Reference `accessing_fields' on page 88 undefined on input line 4672. [88] [89] LaTeX Warning: Reference `object_Protein' on page 90 undefined on input line 47 95. LaTeX Warning: Reference `accessing_fields' on page 90 undefined on input line 4802. [90] LaTeX Warning: Reference `object_ProteinDB' on page 91 undefined on input line 4852. LaTeX Warning: Reference `accessing_fields' on page 91 undefined on input line 4909. [91] LaTeX Warning: Reference `object_RandomProteinDB' on page 92 undefined on input line 4954. LaTeX Warning: Reference `object_RandomDNADB' on page 92 undefined on input lin e 4956. LaTeX Warning: Reference `accessing_fields' on page 92 undefined on input line 4963. LaTeX Warning: Reference `accessing_fields' on page 92 undefined on input line 4984. [92] LaTeX Warning: Reference `object_RandomModelDNA' on page 93 undefined on input line 5006. LaTeX Warning: Reference `object_RandomModel' on page 93 undefined on input lin e 5008. LaTeX Warning: Reference `accessing_fields' on page 93 undefined on input line 5046. [93] LaTeX Warning: Reference `accessing_fields' on page 94 undefined on input line 5061. LaTeX Warning: Reference `object_Sequence' on page 94 undefined on input line 5 077. LaTeX Warning: Reference `object_SequenceSet' on page 94 undefined on input lin e 5079. [94] LaTeX Warning: Reference `accessing_fields' on page 95 undefined on input line 5143. [95] Overfull \hbox (16.34366pt too wide) in paragraph at lines 5203--5204 []\OT1/cmtt/m/n/10 Wise2[]force[]to[]dna[]Sequence (seq,fraction,number[]of[]co nver) [96] [97] [98] [99] [100] [101] LaTeX Warning: Reference `accessing_fields' on page 102 undefined on input line 5540. [102] [103] LaTeX Warning: Reference `object_SequenceDB' on page 104 undefined on input lin e 5629. LaTeX Warning: Reference `object_FileSource' on page 104 undefined on input lin e 5631. LaTeX Warning: Reference `accessing_fields' on page 104 undefined on input line 5658. [104] LaTeX Warning: Reference `accessing_fields' on page 105 undefined on input line 5719. LaTeX Warning: Reference `object_Exon' on page 105 undefined on input line 5745 . LaTeX Warning: Reference `object_Transcript' on page 105 undefined on input lin e 5747. [105] LaTeX Warning: Reference `accessing_fields' on page 106 undefined on input line 5754. LaTeX Warning: Reference `accessing_fields' on page 106 undefined on input line 5777. [106] LaTeX Warning: Reference `object_Translation' on page 107 undefined on input li ne 5846. LaTeX Warning: Reference `accessing_fields' on page 107 undefined on input line 5853. Overfull \hbox (24.01358pt too wide) in paragraph at lines 5872--5879 \OT1/cmr/m/n/10 have any se-quence in it. When se-quence is asked for by get[]P rotein[]from[]Translation() [107] [108] (./api.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on api.pdf (108 pages, 304030 bytes). Transcript written on api.log. cd docs && pdflatex api.tex This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013/Debian) restricted \write18 enabled. entering extended mode (./api.tex LaTeX2e <2011/06/27> Babel <3.9f> and hyphenation patterns for 2 languages loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/latex209.def Entering LaTeX 2.09 COMPATIBILITY MODE ************************************************************* !!WARNING!! !!WARNING!! !!WARNING!! !!WARNING!! This mode attempts to provide an emulation of the LaTeX 2.09 author environment so that OLD documents can be successfully processed. It should NOT be used for NEW documents! New documents should use Standard LaTeX conventions and start with the \documentclass command. Compatibility mode is UNLIKELY TO WORK with LaTeX 2.09 style files that change any internal macros, especially not with those that change the FONT SELECTION or OUTPUT ROUTINES. Therefore such style files MUST BE UPDATED to use Current Standard LaTeX: LaTeX2e. If you suspect that you may be using such a style file, which is probably very, very old by now, then you should attempt to get it updated by sending a copy of this error message to the author of that file. ************************************************************* (/usr/share/texlive/texmf-dist/tex/latex/base/tracefnt.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/latexsym.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (./api.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ulasy.fd) [1{/var/lib/texmf/fonts /map/pdftex/updmap/pdftex.map}] (./api.toc [2] [3] [4] [5] [6] [7] [8] [9]) [10] [11] Overfull \hbox (1.49698pt too wide) in paragraph at lines 107--107 [] \OT1/cmtt/m/n/10 print "You must give a file to revcom for a reverse to w ork!";[] [12] [13] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [14] LaTeX Warning: Reference `object_GeneFrequency' on page 15 undefined on input l ine 231. LaTeX Warning: Reference `module_gwrap' on page 15 undefined on input line 234. LaTeX Warning: Reference `module_gwrap' on page 15 undefined on input line 235. Overfull \hbox (21.30891pt too wide) in paragraph at lines 235--236 []\OT1/cmr/m/n/10 Build an en-tire pa-ram-e-ter set for ge-newise us-ing Wise2: :GeneParameter21[]wrap LaTeX Warning: Reference `module_gwrap' on page 15 undefined on input line 236. LaTeX Warning: Reference `module_gwrap' on page 15 undefined on input line 237. [15] [16] [17] LaTeX Warning: Reference `module_gwrap' on page 18 undefined on input line 387. [18] LaTeX Warning: Reference `module_codonmat' on page 19 undefined on input line 4 24. [19] LaTeX Warning: Reference `module_dbimpl' on page 20 undefined on input line 433 . [20] Overfull \hbox (62.7533pt too wide) in paragraph at lines 509--510 []\OT1/cmtt/m/n/10 Wise2[]make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap, text,dpri) Overfull \hbox (40.0498pt too wide) in paragraph at lines 510--511 []\OT1/cmtt/m/n/10 &Wise2::make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap ,text,dpri) [21] Overfull \hbox (335.96082pt too wide) in paragraph at lines 571--572 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]TSM[]estwise (tdb,cdb,cp,cm,rmd,use[]sy n,alg,bits[]cutoff,allN,flat[]insert,report[]level,die[]on[]error,dbsi) Overfull \hbox (313.25732pt too wide) in paragraph at lines 572--573 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]TSM[]estwise (tdb,cdb,cp,cm,rmd,use[]s yn,alg,bits[]cutoff,allN,flat[]insert,report[]level,die[]on[]error,dbsi) [22] Overfull \hbox (329.87091pt too wide) in paragraph at lines 598--599 []\OT1/cmtt/m/n/10 Wise2[]AlnBlock[]from[]Protein[]estwise[]wrap (pro,cdna,cp,c m,ct,comp,gap,ext,is[]global,rmd,alg,rm,use[]syn,allN,dpri,palpoi) Overfull \hbox (270.41774pt too wide) in paragraph at lines 599--600 []\OT1/cmtt/m/n/10 &Wise2::AlnBlock[]from[]Protein[]estwise[]wrap (pro,cdna,cp, cm,ct,comp,gap,ext,is[]global,rmd,alg,rm,use[]syn,allN,dpri) [23] Overfull \hbox (265.40146pt too wide) in paragraph at lines 632--633 []\OT1/cmtt/m/n/10 Wise2[]AlnBlock[]from[]TSM[]estwise[]wrap (tsm,cdna,cp,cm,ct ,rmd,alg,use[]syn,force[]flat[]insert,allN,dpri,palpoi) Overfull \hbox (205.94829pt too wide) in paragraph at lines 633--634 []\OT1/cmtt/m/n/10 &Wise2::AlnBlock[]from[]TSM[]estwise[]wrap (tsm,cdna,cp,cm,c t,rmd,alg,use[]syn,force[]flat[]insert,allN,dpri) [24] Overfull \hbox (47.00343pt too wide) in paragraph at lines 680--681 []\OT1/cmtt/m/n/10 Wise2[]protein2genomic[]ascii[]display (alb,p,gen,ct,name,ma in,ofp) Overfull \hbox (24.29994pt too wide) in paragraph at lines 681--682 []\OT1/cmtt/m/n/10 &Wise2::protein2genomic[]ascii[]display (alb,p,gen,ct,name,m ain,ofp) Overfull \hbox (188.7522pt too wide) in paragraph at lines 701--702 []\OT1/cmtt/m/n/10 Wise2[]protcdna[]ascii[]display (alb,protsequence,protname,p rotoff,cdna,ct,name,main,mult,ofp) Overfull \hbox (166.0487pt too wide) in paragraph at lines 702--703 []\OT1/cmtt/m/n/10 &Wise2::protcdna[]ascii[]display (alb,protsequence,protname, protoff,cdna,ct,name,main,mult,ofp) [25] [26] Overfull \hbox (1.40793pt too wide) in paragraph at lines 793--794 []\OT1/cmr/m/n/10 transition[GENEFREQUENCY21[]TRANSITION[]LEN] Type [dou-ble : Scalar] [27] [28] Overfull \hbox (71.7832pt too wide) in paragraph at lines 914--915 []\OT1/cmtt/m/n/10 Wise2[]MatchSummarySet[]from[]AlnBlock[]estwise (alb,qname,o ffset,target) Overfull \hbox (1.83012pt too wide) in paragraph at lines 915--916 []\OT1/cmtt/m/n/10 &Wise2::MatchSummarySet::MatchSummarySet[]from[]AlnBlock[]es twise Overfull \hbox (62.22557pt too wide) in paragraph at lines 917--918 []\OT1/cmtt/m/n/10 $obj->MatchSummarySet[]from[]AlnBlock[]estwise(qname,offset, target) [29] Overfull \hbox (82.28311pt too wide) in paragraph at lines 940--941 []\OT1/cmtt/m/n/10 Wise2[]MatchSummarySet[]from[]AlnBlock[]genewise (alb,qname, protoff,target) Overfull \hbox (7.08008pt too wide) in paragraph at lines 941--942 []\OT1/cmtt/m/n/10 &Wise2::MatchSummarySet::MatchSummarySet[]from[]AlnBlock[]ge newise Overfull \hbox (72.72548pt too wide) in paragraph at lines 943--944 []\OT1/cmtt/m/n/10 $obj->MatchSummarySet[]from[]AlnBlock[]genewise(qname,protof f,target) [30] [31] Overfull \hbox (92.78302pt too wide) in paragraph at lines 1074--1075 []\OT1/cmtt/m/n/10 Wise2[]write[]pretty[]str[]align (alb,qname,query,tname,targ et,name,main,ofp) Overfull \hbox (70.07953pt too wide) in paragraph at lines 1075--1076 []\OT1/cmtt/m/n/10 &Wise2::write[]pretty[]str[]align (alb,qname,query,tname,tar get,name,main,ofp) [32] Overfull \hbox (3.5338pt too wide) in paragraph at lines 1117--1118 []\OT1/cmtt/m/n/10 Wise2[]write[]pretty[]Protein[]align (alb,q,t,name,main,ofp) [33] Overfull \hbox (29.5499pt too wide) in paragraph at lines 1190--1191 []\OT1/cmtt/m/n/10 &Wise2::DnaSequenceHitList::read[]MSPcrunch[]DnaSequenceHitL ist (ifp) [34] Overfull \hbox (99.50298pt too wide) in paragraph at lines 1248--1249 []\OT1/cmtt/m/n/10 Wise2[]Align[]strings[]ProteinSmithWaterman (one,two,comp,ga p,ext,dpenv,dpri) Overfull \hbox (76.79948pt too wide) in paragraph at lines 1249--1250 []\OT1/cmtt/m/n/10 &Wise2::Align[]strings[]ProteinSmithWaterman (one,two,comp,g ap,ext,dpenv,dpri) [35] Overfull \hbox (110.00288pt too wide) in paragraph at lines 1273--1274 []\OT1/cmtt/m/n/10 Wise2[]Align[]Sequences[]ProteinSmithWaterman (one,two,comp, gap,ext,dpenv,dpri) Overfull \hbox (87.2994pt too wide) in paragraph at lines 1274--1275 []\OT1/cmtt/m/n/10 &Wise2::Align[]Sequences[]ProteinSmithWaterman (one,two,comp ,gap,ext,dpenv,dpri) Overfull \hbox (7.58401pt too wide) in paragraph at lines 1286--1287 []\OT1/cmr/m/n/10 [OWNER] new AlnBlock struc-ture rep-re-sent-ing the align-men t [AlnBlock [36] Overfull \hbox (68.00325pt too wide) in paragraph at lines 1307--1308 []\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]SmithWaterman (one,two,comp,gap,ext, dpenv,dpri) Overfull \hbox (45.29976pt too wide) in paragraph at lines 1308--1309 []\OT1/cmtt/m/n/10 &Wise2::Align[]Proteins[]SmithWaterman (one,two,comp,gap,ext ,dpenv,dpri) Overfull \hbox (5.0038pt too wide) in paragraph at lines 1334--1335 []\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]ABC (one,two,comp,a,b,c,dpenv,dpri) [37] Overfull \hbox (47.00343pt too wide) in paragraph at lines 1355--1356 []\OT1/cmtt/m/n/10 Wise2[]Align[]Sequences[]ProteinABC (one,two,comp,a,b,c,dpen v,dpri) Overfull \hbox (24.29994pt too wide) in paragraph at lines 1356--1357 []\OT1/cmtt/m/n/10 &Wise2::Align[]Sequences[]ProteinABC (one,two,comp,a,b,c,dpe nv,dpri) Overfull \hbox (86.01088pt too wide) in paragraph at lines 1371--1374 \OT1/cmr/m/n/10 Align[]Sequences[]ProteinABC this func-tion is anal-o-gous to A lign[]Sequences[]ProteinSmithWaterman Overfull \hbox (240.62169pt too wide) in paragraph at lines 1378--1379 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinSW (querydb,targetdb,comp,gap,ex t,bits[]cutoff,report[]level,die[]on[]error,dbsi) Overfull \hbox (217.9182pt too wide) in paragraph at lines 1379--1380 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinSW (querydb,targetdb,comp,gap,e xt,bits[]cutoff,report[]level,die[]on[]error,dbsi) [38] Overfull \hbox (235.37173pt too wide) in paragraph at lines 1400--1401 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b,c ,bits[]cutoff,report[]level,die[]on[]error,dbsi) Overfull \hbox (212.66824pt too wide) in paragraph at lines 1401--1402 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b, c,bits[]cutoff,report[]level,die[]on[]error,dbsi) [39] Overfull \hbox (359.90063pt too wide) in paragraph at lines 1423--1424 []\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinBA (querydb,targetdb,comp,bentry ,bexit,bfor[]trans,b[]self[]trans,b3exit,bits[]cutoff,report[]level,dbsi) Overfull \hbox (337.19714pt too wide) in paragraph at lines 1424--1425 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinBA (querydb,targetdb,comp,bentr y,bexit,bfor[]trans,b[]self[]trans,b3exit,bits[]cutoff,report[]level,dbsi) [40] Overfull \hbox (15.42177pt too wide) in paragraph at lines 1487--1488 []\OT1/cmr/m/n/10 reload[]generic Type [Three-State-Model * (*reload[]generic)( ThreeStateDB * tdb,int Overfull \hbox (3.42192pt too wide) in paragraph at lines 1494--1495 []\OT1/cmr/m/n/10 dataentry[]add Type [boolean (*dataen-try[]add)(ThreeStateDB * tdb,DataEntry Overfull \hbox (41.78299pt too wide) in paragraph at lines 1498--1499 []\OT1/cmr/m/n/10 index[]generic Type [Three-State-Model * (*in-dex[]generic)(T hreeStateDB *tdb,DataEntry [41] Overfull \hbox (29.5499pt too wide) in paragraph at lines 1569--1570 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateDB::new[]proteindb[]ThreeStateDB (sdb,comp ,gap,ext) [42] [43] [44] Overfull \hbox (16.10999pt too wide) in paragraph at lines 1702--1703 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::force[]global[]model (tsm,prob[]int o[]model) Overfull \hbox (102.65288pt too wide) in paragraph at lines 1722--1723 []\OT1/cmtt/m/n/10 Wise2[]force[]weighted[]local[]model (tsm,prob[]into[]model, ratio[]start,ratio[]end) Overfull \hbox (169.19861pt too wide) in paragraph at lines 1723--1724 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::force[]weighted[]local[]model (tsm, prob[]into[]model,ratio[]start,ratio[]end) Overfull \hbox (93.09525pt too wide) in paragraph at lines 1725--1726 []\OT1/cmtt/m/n/10 $obj->force[]weighted[]local[]model(prob[]into[]model,ratio[ ]start,ratio[]end) Overfull \hbox (49.31339pt too wide) in paragraph at lines 1745--1746 []\OT1/cmtt/m/n/10 Wise2[]ThreeStateModel[]from[]half[]bit[]Sequence (pro,mat,r m,gap,ext) [45] Overfull \hbox (5.61008pt too wide) in paragraph at lines 1746--1747 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::ThreeStateModel[]from[]half[]bit[]S equence Overfull \hbox (39.75575pt too wide) in paragraph at lines 1748--1749 []\OT1/cmtt/m/n/10 $obj->ThreeStateModel[]from[]half[]bit[]Sequence(mat,rm,gap, ext) Overfull \hbox (51.38966pt too wide) in paragraph at lines 1772--1773 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::write[]HMMer[]1[]7[]ascii[]ThreeSta teModel (tsm,ofp) [46] Overfull \hbox (6.8248pt too wide) in paragraph at lines 1839--1846 \OT1/cmr/m/n/10 AlnBlock is the main rep-re-sen-ta-tion of align-ments from Dy- na-mite. Each AlnBlock [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] Overfull \hbox (12.33003pt too wide) in paragraph at lines 2782--2783 []\OT1/cmtt/m/n/10 &Wise2::CodonMapper::sprinkle[]errors[]over[]CodonMapper (cm ,error) [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] Overfull \hbox (0.5938pt too wide) in paragraph at lines 3353--3354 []\OT1/cmtt/m/n/10 Wise2[]Genomic[]from[]Sequence[]Nheuristic (seq,length[]of[] N) [74] [75] [76] Overfull \hbox (65.9032pt too wide) in paragraph at lines 3539--3540 []\OT1/cmtt/m/n/10 Wise2[]new[]GenomicDB[]from[]single[]seq (gen,cses,score[]in []repeat[]coding) Overfull \hbox (43.1997pt too wide) in paragraph at lines 3540--3541 []\OT1/cmtt/m/n/10 &Wise2::new[]GenomicDB[]from[]single[]seq (gen,cses,score[]i n[]repeat[]coding) Overfull \hbox (41.12343pt too wide) in paragraph at lines 3556--3557 []\OT1/cmtt/m/n/10 Wise2[]new[]GenomicDB (seqdb,cses,length[]of[]N,repeat[]in[] cds[]score) Overfull \hbox (18.41994pt too wide) in paragraph at lines 3557--3558 []\OT1/cmtt/m/n/10 &Wise2::new[]GenomicDB (seqdb,cses,length[]of[]N,repeat[]in[ ]cds[]score) [77] [78] [79] Overfull \hbox (1.83012pt too wide) in paragraph at lines 3712--3713 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::read[]EMBL[]GenomicRegion[]file (file name) [80] Overfull \hbox (7.08008pt too wide) in paragraph at lines 3765--3766 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::show[]ace[]GenomicRegion (gr,seq[]nam e,ofp) Overfull \hbox (3.5338pt too wide) in paragraph at lines 3790--3791 []\OT1/cmtt/m/n/10 Wise2[]show[]pretty[]GenomicRegion (gr,show[]supporting,ofp) Overfull \hbox (59.57962pt too wide) in paragraph at lines 3791--3792 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::show[]pretty[]GenomicRegion (gr,show[ ]supporting,ofp) [81] [82] [83] Overfull \hbox (32.9967pt too wide) in paragraph at lines 3956--3956 [] \OT1/cmtt/m/n/10 b) cooperation with future versions of histogram.c would be possible.[] [84] [85] [86] Overfull \hbox (123.4428pt too wide) in paragraph at lines 4158--4159 []\OT1/cmtt/m/n/10 Wise2[]ExtremeValueSetHistogram (h,mu,lambda,lowbound,highbo und,wonka,ndegrees) Overfull \hbox (67.76958pt too wide) in paragraph at lines 4159--4160 []\OT1/cmtt/m/n/10 &Wise2::Histogram::set[]EVD (h,mu,lambda,lowbound,highbound, wonka,ndegrees) Overfull \hbox (33.66585pt too wide) in paragraph at lines 4161--4162 []\OT1/cmtt/m/n/10 $obj->set[]EVD(mu,lambda,lowbound,highbound,wonka,ndegrees) [87] [88] [89] Overfull \hbox (30.97293pt too wide) in paragraph at lines 4335--4336 []\OT1/cmr/m/n/10 should[]store Type [boolean (*should[]store)(int given[]score ,double in-ter-nal[]score[]level) [90] [91] [92] [93] [94] [95] [96] [97] [98] [99] [100] [101] [102] [103] Overfull \hbox (16.34366pt too wide) in paragraph at lines 5203--5204 []\OT1/cmtt/m/n/10 Wise2[]force[]to[]dna[]Sequence (seq,fraction,number[]of[]co nver) [104] [105] [106] [107] [108] [109] [110] [111] [112] [113] [114] Overfull \hbox (24.01358pt too wide) in paragraph at lines 5872--5879 \OT1/cmr/m/n/10 have any se-quence in it. When se-quence is asked for by get[]P rotein[]from[]Translation() [115] [116] (./api.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on api.pdf (116 pages, 318619 bytes). Transcript written on api.log. cd docs && pdflatex dynamite.tex This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013/Debian) restricted \write18 enabled. entering extended mode (./dynamite.tex LaTeX2e <2011/06/27> Babel <3.9f> and hyphenation patterns for 2 languages loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/latex209.def Entering LaTeX 2.09 COMPATIBILITY MODE ************************************************************* !!WARNING!! !!WARNING!! !!WARNING!! !!WARNING!! This mode attempts to provide an emulation of the LaTeX 2.09 author environment so that OLD documents can be successfully processed. It should NOT be used for NEW documents! New documents should use Standard LaTeX conventions and start with the \documentclass command. Compatibility mode is UNLIKELY TO WORK with LaTeX 2.09 style files that change any internal macros, especially not with those that change the FONT SELECTION or OUTPUT ROUTINES. Therefore such style files MUST BE UPDATED to use Current Standard LaTeX: LaTeX2e. If you suspect that you may be using such a style file, which is probably very, very old by now, then you should attempt to get it updated by sending a copy of this error message to the author of that file. ************************************************************* (/usr/share/texlive/texmf-dist/tex/latex/base/tracefnt.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/latexsym.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) No file dynamite.aux. (/usr/share/texlive/texmf-dist/tex/latex/base/ulasy.fd) [1{/var/lib/texmf/fonts /map/pdftex/updmap/pdftex.map}] No file dynamite.toc. [2] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [3] LaTeX Warning: Reference `own_objects' on page 4 undefined on input line 75. [4] [5] [6] Overfull \hbox (4.11092pt too wide) in paragraph at lines 251--255 \OT1/cmr/m/n/10 tri-bu-tion from 'ftp://ftp.sanger.ac.uk/pub/birney/dynamite/dy n.x.tar.Z' (where [7] [8] [9] [10] Overfull \hbox (48.74657pt too wide) in paragraph at lines 586--586 [] \OT1/cmtt/m/n/10 fprintf(ofp,"\npsw seq1 seq2\nBoth sequences in fasta format\n"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 586--586 [] \OT1/cmtt/m/n/10 * -g for gap value (an int) - rely on commandline error p rocessing[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 586--586 [] \OT1/cmtt/m/n/10 * -e for ext value (an int) - rely on commandline error p rocessing[] [11] Overfull \hbox (269.24464pt too wide) in paragraph at lines 586--586 [] \OT1/cmtt/m/n/10 if( strip_out_boolean_argument(&argc,argv,"h") == TRUE || strip_out_boolean_argument(&argc,argv,"-help") == TRUE) {[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 586--586 [] \OT1/cmtt/m/n/10 warn("Must have two arguments for sequence 1 and sequenc e 2 %d",argc);[] [12] Overfull \hbox (22.4968pt too wide) in paragraph at lines 586--586 [] \OT1/cmtt/m/n/10 * or WISEPERSONALDIR if it is not present in the current directory.[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 586--586 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 586--586 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 586--586 [] \OT1/cmtt/m/n/10 * If the sequences are small enough then it should use ex plicit memory.[] [13] Overfull \hbox (59.24648pt too wide) in paragraph at lines 586--586 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp ,-gap,-ext,NULL);[] Overfull \hbox (80.24629pt too wide) in paragraph at lines 586--586 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query ->name,target->name);[] [14] Overfull \hbox (48.74657pt too wide) in paragraph at lines 630--630 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 630--630 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 630--630 [] \OT1/cmtt/m/n/10 * If the sequences are small enough then it should use ex plicit memory.[] [15] Overfull \hbox (59.24648pt too wide) in paragraph at lines 630--630 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp ,-gap,-ext,NULL);[] Overfull \hbox (80.24629pt too wide) in paragraph at lines 630--630 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query ->name,target->name);[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 637--637 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp ,-gap,-ext);[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 652--652 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] [16] Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 []\OT1/cmtt/m/n/10 Q22037 EPENLRKIFVGGLTSNTTDDLMREFYSQFGEITDIIVMR DPTTKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 [] \OT1/cmtt/m/n/10 EPE LRK+F+GGL+ TTD+ +R + Q+G +TD +VMR DP TKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 []\OT1/cmtt/m/n/10 ROA1_HUMAN EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMR DPNTKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 []\OT1/cmtt/m/n/10 Q22037 GFVTFSGKTEVDAAMKQRPHIIDGKTVDPKRAVPRDDKN RSESNVSTKR[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 [] \OT1/cmtt/m/n/10 GFVT++ EVDAAM RPH +DG+ V+PKRAV R+D R ++++ K+[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 []\OT1/cmtt/m/n/10 ROA1_HUMAN GFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQ RPGAHLTVKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 []\OT1/cmtt/m/n/10 Q22037 LYVSGVREDHTEDMLTEYFTKYGTVTKSEIILDKATQKP RGFGFVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 [] \OT1/cmtt/m/n/10 ++V G++ED E L +YF +YG + EI+ D+ + K RGF FVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 []\OT1/cmtt/m/n/10 ROA1_HUMAN IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKK RGFAFVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 []\OT1/cmtt/m/n/10 Q22037 HDSVDQCVLQKSHMVNGHRCDVRKGLSKDEMSKAQMNRD RETRGGRSRD[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 736--736 [] \OT1/cmtt/m/n/10 HDSVD+ V+QK H VNGH C+VRK LSK EM+ A ++ GRS[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 []\OT1/cmtt/m/n/10 ROA1_HUMAN HDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASAS---- -SSQRGRSGS[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 []\OT1/cmtt/m/n/10 Q22037 GQRGGYNGGG-GGGGGWGGPAQRGGPGAYGGP-GGGGQG GYGGDYGG--[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 736--736 [] \OT1/cmtt/m/n/10 G GG GGG GG +G G G +GG GGGG G G G Y G[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 []\OT1/cmtt/m/n/10 ROA1_HUMAN GNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSRGGGGYG GSGDGYNGFG[] [17] Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 []\OT1/cmtt/m/n/10 Q22037 GWGQQGGGGQGGWGGPQQQQGGG-GWGQQGGGGQGGWGG PQQQQQGGWG[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 736--736 [] \OT1/cmtt/m/n/10 G GGGG G GG + GG G+G QG G GG G GG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 []\OT1/cmtt/m/n/10 ROA1_HUMAN NDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSG-YGGSGS YDSYNNGGGR[] [18] Overfull \hbox (48.88945pt too wide) in paragraph at lines 791--793 []\OT1/cmr/m/n/10 The align-ment is the set of (i,j,) triples, where sta te is one of (Match,Insert,Delete) [19] [20] [21] Overfull \hbox (17.24684pt too wide) in paragraph at lines 940--940 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 940--940 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 940--940 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 940--940 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] [22] Overfull \hbox (32.64503pt too wide) in paragraph at lines 1013--1017 \OT1/cmr/m/n/10 and GE-NOMIC[]INTRON. No-tice how the source lines to and from GE-NOMIC[]INSERT [23] Overfull \hbox (38.24666pt too wide) in paragraph at lines 1114--1114 []\OT1/cmtt/m/n/10 #define DnaMatrix_Score(dnamat,base1,base2) (dnamat->score[b ase1][base2])[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1114--1114 [] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,i),GENOMIC_BASE(tar get,j))"[] [24] [25] Overfull \hbox (122.24593pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 fprintf(ofp,"\nest2gen est-seq genomic-seq\nBoth sequences in fasta format\n"[] [26] Overfull \hbox (269.24464pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 if( strip_out_boolean_argument(&argc,argv,"h") == TRUE || strip_out_boolean_argument(&argc,argv,"-help") == TRUE) {[] [27] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 warn("Must have two arguments for sequence 1 and sequenc e 2 %d",argc);[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 * To do this we need a cdna ComplexSequenceEvalSet and a genomic one[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 * Really our genomic model should be alot more complex. T he 'default' one[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 * has 0 at GT----AG for 5' and 3' splice sites, and NEGI (= -infinity)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 * We could build up something much better, using complexc onsensi and[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 * other machinery, but not for now . See the genewi se code if you[] [28] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 * cDNA2Gen has alot more parameter space than the paramet ers to this[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 * program. Firstly we are treating errors similarly on ea ch side of the[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 * Secondly there is a rather complex interaction between the gap/extension[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 * of what is thought to be sequencing error and the intro ns. Here we have[] Overfull \hbox (64.49643pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 * one more parameter, and intron open penalty, which can be set, to prevent[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 * One good way to parameterise all this would be to have a probabilistic[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 * model of the processes, derive probabilities and then m ap them to ints[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 * (probability.h has got these mappings, such as Probabil ity2Score).[] Overfull \hbox (101.24611pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_cDNA2Gen(query_cs,target_cs,dm,ga p,-ext,-gap,-ext,0,NULL);[] Overfull \hbox (80.24629pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query ->name,target->name);[] [29] Overfull \hbox (74.99634pt too wide) in paragraph at lines 1340--1340 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_cDNA2Gen(query_cs,target_cs,dm,ga p,-ext,-gap,-ext,0);[] [30] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1377--1377 [] \OT1/cmtt/m/n/10 * To do this we need a cdna ComplexSequenceEvalSet and a genomic one[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1377--1377 [] \OT1/cmtt/m/n/10 * Really our genomic model should be alot more complex. T he 'default' one[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 1377--1377 [] \OT1/cmtt/m/n/10 * has 0 at GT----AG for 5' and 3' splice sites, and NEGI (= -infinity)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1377--1377 [] \OT1/cmtt/m/n/10 * We could build up something much better, using complexc onsensi and[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1377--1377 [] \OT1/cmtt/m/n/10 * other machinery, but not for now . See the genewi se code if you[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1377--1377 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1377--1377 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNCPA1 1 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GATGGT-TAT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 [] \OT1/cmtt/m/n/10 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GAT T T T[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNRNPA 2132 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GAT--TAT-T[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNCPA1 49 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] [31] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 [] \OT1/cmtt/m/n/10 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNRNPA 2178 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNCPA1 98 CAGTGGCAAGAAAAGGGGCTTTGCCT-TAGTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 [] \OT1/cmtt/m/n/10 CAGTGGCAAGAAAAGGGGCTTTGCCT T GTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNRNPA 2227 CAGTGGCAAGAAAAGGGGCTTTGCCTTT-GTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNCPA1 146 CTCCGTGGATAAGATTGTCA TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 [] \OT1/cmtt/m/n/10 CTCCGTGGATAAGATTGTCA TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNRNPA 2275 CTCCGTGGATAAGATTGTCA<-2295:2387->TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNCPA1 182 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 [] \OT1/cmtt/m/n/10 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNRNPA 2404 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNCPA1 231 ATGGCTAGTGCTTCATCCAGCCAAAGAG GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 [] \OT1/cmtt/m/n/10 ATGGCTAGTGCTTCATCCAGCCAAAGAG GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNRNPA 2453 ATGGCTAGTGCTTCATCCAGCCAAAGAG<-2481:2566 ->GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNCPA1 267 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 [] \OT1/cmtt/m/n/10 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNRNPA 2575 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNRNPA 2624 ACAACTTCGGTCGTGGAGGAAACTTCAGTGGTCGTG<-2 660:2793->[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNCPA1 352 GTNG-CTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 [] \OT1/cmtt/m/n/10 GT G CTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNRNPA 2794 GT-GGCTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNCPA1 400 ATGGCTATAATGGATTTGGCAATGATG GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 [] \OT1/cmtt/m/n/10 ATGGCTATAATGGATTTGGCAATGATG GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNRNPA 2842 ATGGCTATAATGGATTTGGCAATGATG<-2869:3805- >GAAGCAATT[] [32] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNCPA1 436 TTGGAGGTGGTGGAAGCTACAATGATTTTGGG--tttat gcA-CAATCA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 [] \OT1/cmtt/m/n/10 TTGGAGGTGGTGGAAGCTACAATGATTTTGGG ++ + +A CAATCA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNRNPA 3815 TTGGAGGTGGTGGAAGCTACAATGATTTTGGGAATT-A- -CAACAATCA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNCPA1 482 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 [] \OT1/cmtt/m/n/10 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNRNPA 3861 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNCPA1 531 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 [] \OT1/cmtt/m/n/10 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNRNPA 3910 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNCPA1 580 AAG GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 [] \OT1/cmtt/m/n/10 AAG GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNRNPA 3959 AAG<-3962:4251->GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] [33] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1570--1570 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1570--1570 []\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o f_sequence"[] [34] [35] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1598--1598 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 1632--1632 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_MyProteinSW(seqone,seqtwo,mat,-12, -2,NULL);[] Overfull \hbox (127.49588pt too wide) in paragraph at lines 1632--1632 [] \OT1/cmtt/m/n/10 fprintf(stdout,"%d,%d are matched with score %d\n",uni t->i+1,unit->j+1,unit->score);[] [36] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1725--1725 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1725--1725 []\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o f_sequence"[] [37] [38] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1847--1847 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1847--1847 []\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o f_sequence"[] [39] Overfull \hbox (258.74474pt too wide) in paragraph at lines 1847--1847 [] \OT1/cmtt/m/n/10 calc="ALPHA_SEQ_SCORE(query,i) + ALPHA_SEQ_SCORE(target,j) + mat_alpha.comp[SEQ_POS(query,i)][SEQ_POS(target,j)]"[] [40] [41] Overfull \hbox (20.54509pt too wide) in paragraph at lines 1909--1910 []\OT1/cmr/m/n/10 The macro Dna-Ma-trix[]Score which is de-fined at the top of the cdna2genomic.dy [42] Overfull \hbox (17.24684pt too wide) in paragraph at lines 1926--1926 [] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,i),GENOMIC_CODON(ta rget,j))"[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1942--1942 [] \OT1/cmtt/m/n/10 Mis-type in argument 3 of DNA\_MAT\_SCORE: wanted [b ase] got [codon][] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1953--1953 [] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,j),GENOMIC_BASE(tar get,j))"[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 1965--1965 [] \OT1/cmtt/m/n/10 For function CDNA\_BASE, you have arguments j and qu ery, which do not[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1965--1965 []\OT1/cmtt/m/n/10 expect to paired directly in a function. This is just a warn ing that[] [43] Overfull \hbox (17.24684pt too wide) in paragraph at lines 2012--2012 [] \OT1/cmtt/m/n/10 throw_warning("Letter %c does not exist in comparison matr ix",one);[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 2012--2012 [] \OT1/cmtt/m/n/10 throw_warning("Letter %c does not exist in comparison matr ix",two);[] [44] [45] Overfull \hbox (74.99634pt too wide) in paragraph at lines 2253--2253 [] \OT1/cmtt/m/n/10 fprintf(stdout,"dbsearch [options] \n");[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 2253--2253 [] \OT1/cmtt/m/n/10 /** add more options here sometime, eg comp matrix and gap penalty*/[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 2253--2253 [] \OT1/cmtt/m/n/10 /** print out dbsearch options. We don't know here what im plementations are[] Overfull \hbox (74.99634pt too wide) in paragraph at lines 2253--2253 [] \OT1/cmtt/m/n/10 either possible or how they are specified. Of course, there is the problem[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 2253--2253 [] \OT1/cmtt/m/n/10 that we could clash our options with the dbsearchimpl options, but that[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 2253--2253 [] \OT1/cmtt/m/n/10 is not too likely, and this makes this program future proof wrt to new[] [46] Overfull \hbox (43.49661pt too wide) in paragraph at lines 2253--2253 [] \OT1/cmtt/m/n/10 * care about which implementation is used, and does not k now either (!)[] [47] Overfull \hbox (106.49606pt too wide) in paragraph at lines 2253--2253 [] \OT1/cmtt/m/n/10 /* 10 means a score cutoff of 10, -1 means don't report on stderr search progress */[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 2253--2253 [] \OT1/cmtt/m/n/10 if( search_ProteinSW(dbsi,out,querydb,prodb,mat,-12,-2) != SEARCH_OK )[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 2253--2253 [] \OT1/cmtt/m/n/10 fatal("Some sort of error in the database search. Dieing ungracefully");[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 2253--2253 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] [48] Overfull \hbox (174.74547pt too wide) in paragraph at lines 2253--2253 [] \OT1/cmtt/m/n/10 fprintf(stdout,"Comparison to %s was %d score\n",out-> ds[i]->target->name,out->ds[i]->score);[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 2253--2253 [] \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta rget);[] Overfull \hbox (69.74638pt too wide) in paragraph at lines 2253--2253 []\OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s",te mp->baseseq->name);[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 2253--2253 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs, mat,-12,-2,NULL);[] Overfull \hbox (95.99615pt too wide) in paragraph at lines 2253--2253 []\OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query->na me,temp->baseseq->name);[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 2253--2253 [] \OT1/cmtt/m/n/10 write_pretty_seq_align(alb,query,temp->baseseq,15,50,s tdout);[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 2261--2261 [] \OT1/cmtt/m/n/10 if( search_ProteinSW(dbsi,out,querydb,prodb,mat,-12,-2) != SEARCH_OK )[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 2261--2261 [] \OT1/cmtt/m/n/10 fatal("Some sort of error in the database search. Dieing ungracefully");[] [49] Overfull \hbox (1.49698pt too wide) in paragraph at lines 2290--2290 [] \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta rget);[] [50] [51] [52] [53] [54] Overfull \hbox (1.32472pt too wide) in paragraph at lines 2526--2532 \OT1/cmr/m/n/10 de-scribed by a "state...endstate" multi-line block. Within eac h "state...endstate" [55] [56] [57] [58] [59] Overfull \hbox (1.75064pt too wide) in paragraph at lines 2770--2774 \OT1/cmr/m/n/10 Dy-na-mite file: for ex-am-ple the fol-low-ing er-ror was made by mistyp-ing ``MATCH'' Overfull \hbox (59.24648pt too wide) in paragraph at lines 2790--2790 [] \OT1/cmtt/m/n/10 In matrix ProteinSW - State MATCH asks for source MA TCH2 but there is[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 2790--2790 [] \OT1/cmtt/m/n/10 Failing simple cross-checks, aborting before calc-li ne parsing[] [60] [61] [62] (./dynamite.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on dynamite.pdf (62 pages, 214242 bytes). Transcript written on dynamite.log. cd docs && pdflatex dynamite.tex This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013/Debian) restricted \write18 enabled. entering extended mode (./dynamite.tex LaTeX2e <2011/06/27> Babel <3.9f> and hyphenation patterns for 2 languages loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/latex209.def Entering LaTeX 2.09 COMPATIBILITY MODE ************************************************************* !!WARNING!! !!WARNING!! !!WARNING!! !!WARNING!! This mode attempts to provide an emulation of the LaTeX 2.09 author environment so that OLD documents can be successfully processed. It should NOT be used for NEW documents! New documents should use Standard LaTeX conventions and start with the \documentclass command. Compatibility mode is UNLIKELY TO WORK with LaTeX 2.09 style files that change any internal macros, especially not with those that change the FONT SELECTION or OUTPUT ROUTINES. Therefore such style files MUST BE UPDATED to use Current Standard LaTeX: LaTeX2e. If you suspect that you may be using such a style file, which is probably very, very old by now, then you should attempt to get it updated by sending a copy of this error message to the author of that file. ************************************************************* (/usr/share/texlive/texmf-dist/tex/latex/base/tracefnt.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/latexsym.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (./dynamite.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ulasy.fd) [1{/var/lib/texmf/fonts /map/pdftex/updmap/pdftex.map}] (./dynamite.toc [2] Overfull \hbox (8.02837pt too wide) in paragraph at lines 50--50 [][] []\OT1/cmr/m/n/10 [Dynamite Level] Did not un-der-stand line [ source MAT CH]. ) [3] [4] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [5] [6] [7] [8] Overfull \hbox (4.11092pt too wide) in paragraph at lines 251--255 \OT1/cmr/m/n/10 tri-bu-tion from 'ftp://ftp.sanger.ac.uk/pub/birney/dynamite/dy n.x.tar.Z' (where [9] [10] [11] [12] Overfull \hbox (48.74657pt too wide) in paragraph at lines 586--586 [] \OT1/cmtt/m/n/10 fprintf(ofp,"\npsw seq1 seq2\nBoth sequences in fasta format\n"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 586--586 [] \OT1/cmtt/m/n/10 * -g for gap value (an int) - rely on commandline error p rocessing[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 586--586 [] \OT1/cmtt/m/n/10 * -e for ext value (an int) - rely on commandline error p rocessing[] [13] Overfull \hbox (269.24464pt too wide) in paragraph at lines 586--586 [] \OT1/cmtt/m/n/10 if( strip_out_boolean_argument(&argc,argv,"h") == TRUE || strip_out_boolean_argument(&argc,argv,"-help") == TRUE) {[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 586--586 [] \OT1/cmtt/m/n/10 warn("Must have two arguments for sequence 1 and sequenc e 2 %d",argc);[] [14] Overfull \hbox (22.4968pt too wide) in paragraph at lines 586--586 [] \OT1/cmtt/m/n/10 * or WISEPERSONALDIR if it is not present in the current directory.[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 586--586 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 586--586 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 586--586 [] \OT1/cmtt/m/n/10 * If the sequences are small enough then it should use ex plicit memory.[] [15] Overfull \hbox (59.24648pt too wide) in paragraph at lines 586--586 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp ,-gap,-ext,NULL);[] Overfull \hbox (80.24629pt too wide) in paragraph at lines 586--586 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query ->name,target->name);[] [16] Overfull \hbox (48.74657pt too wide) in paragraph at lines 630--630 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 630--630 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 630--630 [] \OT1/cmtt/m/n/10 * If the sequences are small enough then it should use ex plicit memory.[] [17] Overfull \hbox (59.24648pt too wide) in paragraph at lines 630--630 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp ,-gap,-ext,NULL);[] Overfull \hbox (80.24629pt too wide) in paragraph at lines 630--630 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query ->name,target->name);[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 637--637 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp ,-gap,-ext);[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 652--652 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] [18] Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 []\OT1/cmtt/m/n/10 Q22037 EPENLRKIFVGGLTSNTTDDLMREFYSQFGEITDIIVMR DPTTKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 [] \OT1/cmtt/m/n/10 EPE LRK+F+GGL+ TTD+ +R + Q+G +TD +VMR DP TKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 []\OT1/cmtt/m/n/10 ROA1_HUMAN EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMR DPNTKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 []\OT1/cmtt/m/n/10 Q22037 GFVTFSGKTEVDAAMKQRPHIIDGKTVDPKRAVPRDDKN RSESNVSTKR[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 [] \OT1/cmtt/m/n/10 GFVT++ EVDAAM RPH +DG+ V+PKRAV R+D R ++++ K+[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 []\OT1/cmtt/m/n/10 ROA1_HUMAN GFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQ RPGAHLTVKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 []\OT1/cmtt/m/n/10 Q22037 LYVSGVREDHTEDMLTEYFTKYGTVTKSEIILDKATQKP RGFGFVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 [] \OT1/cmtt/m/n/10 ++V G++ED E L +YF +YG + EI+ D+ + K RGF FVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 []\OT1/cmtt/m/n/10 ROA1_HUMAN IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKK RGFAFVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 []\OT1/cmtt/m/n/10 Q22037 HDSVDQCVLQKSHMVNGHRCDVRKGLSKDEMSKAQMNRD RETRGGRSRD[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 736--736 [] \OT1/cmtt/m/n/10 HDSVD+ V+QK H VNGH C+VRK LSK EM+ A ++ GRS[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 []\OT1/cmtt/m/n/10 ROA1_HUMAN HDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASAS---- -SSQRGRSGS[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 []\OT1/cmtt/m/n/10 Q22037 GQRGGYNGGG-GGGGGWGGPAQRGGPGAYGGP-GGGGQG GYGGDYGG--[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 736--736 [] \OT1/cmtt/m/n/10 G GG GGG GG +G G G +GG GGGG G G G Y G[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 []\OT1/cmtt/m/n/10 ROA1_HUMAN GNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSRGGGGYG GSGDGYNGFG[] [19] Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 []\OT1/cmtt/m/n/10 Q22037 GWGQQGGGGQGGWGGPQQQQGGG-GWGQQGGGGQGGWGG PQQQQQGGWG[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 736--736 [] \OT1/cmtt/m/n/10 G GGGG G GG + GG G+G QG G GG G GG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 736--736 []\OT1/cmtt/m/n/10 ROA1_HUMAN NDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSG-YGGSGS YDSYNNGGGR[] [20] Overfull \hbox (48.88945pt too wide) in paragraph at lines 791--793 []\OT1/cmr/m/n/10 The align-ment is the set of (i,j,) triples, where sta te is one of (Match,Insert,Delete) [21] [22] [23] Overfull \hbox (17.24684pt too wide) in paragraph at lines 940--940 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 940--940 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 940--940 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 940--940 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] [24] Overfull \hbox (32.64503pt too wide) in paragraph at lines 1013--1017 \OT1/cmr/m/n/10 and GE-NOMIC[]INTRON. No-tice how the source lines to and from GE-NOMIC[]INSERT [25] Overfull \hbox (38.24666pt too wide) in paragraph at lines 1114--1114 []\OT1/cmtt/m/n/10 #define DnaMatrix_Score(dnamat,base1,base2) (dnamat->score[b ase1][base2])[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1114--1114 [] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,i),GENOMIC_BASE(tar get,j))"[] [26] [27] Overfull \hbox (122.24593pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 fprintf(ofp,"\nest2gen est-seq genomic-seq\nBoth sequences in fasta format\n"[] [28] Overfull \hbox (269.24464pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 if( strip_out_boolean_argument(&argc,argv,"h") == TRUE || strip_out_boolean_argument(&argc,argv,"-help") == TRUE) {[] [29] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 warn("Must have two arguments for sequence 1 and sequenc e 2 %d",argc);[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 * To do this we need a cdna ComplexSequenceEvalSet and a genomic one[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 * Really our genomic model should be alot more complex. T he 'default' one[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 * has 0 at GT----AG for 5' and 3' splice sites, and NEGI (= -infinity)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 * We could build up something much better, using complexc onsensi and[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 * other machinery, but not for now . See the genewi se code if you[] [30] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 * cDNA2Gen has alot more parameter space than the paramet ers to this[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 * program. Firstly we are treating errors similarly on ea ch side of the[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 * Secondly there is a rather complex interaction between the gap/extension[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 * of what is thought to be sequencing error and the intro ns. Here we have[] Overfull \hbox (64.49643pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 * one more parameter, and intron open penalty, which can be set, to prevent[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 * One good way to parameterise all this would be to have a probabilistic[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 * model of the processes, derive probabilities and then m ap them to ints[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 * (probability.h has got these mappings, such as Probabil ity2Score).[] Overfull \hbox (101.24611pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_cDNA2Gen(query_cs,target_cs,dm,ga p,-ext,-gap,-ext,0,NULL);[] Overfull \hbox (80.24629pt too wide) in paragraph at lines 1333--1333 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query ->name,target->name);[] [31] Overfull \hbox (74.99634pt too wide) in paragraph at lines 1340--1340 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_cDNA2Gen(query_cs,target_cs,dm,ga p,-ext,-gap,-ext,0);[] [32] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1377--1377 [] \OT1/cmtt/m/n/10 * To do this we need a cdna ComplexSequenceEvalSet and a genomic one[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1377--1377 [] \OT1/cmtt/m/n/10 * Really our genomic model should be alot more complex. T he 'default' one[] Overfull \hbox (38.24666pt too wide) in paragraph at lines 1377--1377 [] \OT1/cmtt/m/n/10 * has 0 at GT----AG for 5' and 3' splice sites, and NEGI (= -infinity)[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1377--1377 [] \OT1/cmtt/m/n/10 * We could build up something much better, using complexc onsensi and[] Overfull \hbox (43.49661pt too wide) in paragraph at lines 1377--1377 [] \OT1/cmtt/m/n/10 * other machinery, but not for now . See the genewi se code if you[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 1377--1377 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1377--1377 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",target->name);[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNCPA1 1 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GATGGT-TAT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 [] \OT1/cmtt/m/n/10 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GAT T T T[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNRNPA 2132 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GAT--TAT-T[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNCPA1 49 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] [33] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 [] \OT1/cmtt/m/n/10 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNRNPA 2178 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNCPA1 98 CAGTGGCAAGAAAAGGGGCTTTGCCT-TAGTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 [] \OT1/cmtt/m/n/10 CAGTGGCAAGAAAAGGGGCTTTGCCT T GTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNRNPA 2227 CAGTGGCAAGAAAAGGGGCTTTGCCTTT-GTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNCPA1 146 CTCCGTGGATAAGATTGTCA TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 [] \OT1/cmtt/m/n/10 CTCCGTGGATAAGATTGTCA TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNRNPA 2275 CTCCGTGGATAAGATTGTCA<-2295:2387->TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNCPA1 182 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 [] \OT1/cmtt/m/n/10 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNRNPA 2404 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNCPA1 231 ATGGCTAGTGCTTCATCCAGCCAAAGAG GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 [] \OT1/cmtt/m/n/10 ATGGCTAGTGCTTCATCCAGCCAAAGAG GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNRNPA 2453 ATGGCTAGTGCTTCATCCAGCCAAAGAG<-2481:2566 ->GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNCPA1 267 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 [] \OT1/cmtt/m/n/10 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNRNPA 2575 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNRNPA 2624 ACAACTTCGGTCGTGGAGGAAACTTCAGTGGTCGTG<-2 660:2793->[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNCPA1 352 GTNG-CTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 [] \OT1/cmtt/m/n/10 GT G CTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNRNPA 2794 GT-GGCTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNCPA1 400 ATGGCTATAATGGATTTGGCAATGATG GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 [] \OT1/cmtt/m/n/10 ATGGCTATAATGGATTTGGCAATGATG GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNRNPA 2842 ATGGCTATAATGGATTTGGCAATGATG<-2869:3805- >GAAGCAATT[] [34] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNCPA1 436 TTGGAGGTGGTGGAAGCTACAATGATTTTGGG--tttat gcA-CAATCA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 [] \OT1/cmtt/m/n/10 TTGGAGGTGGTGGAAGCTACAATGATTTTGGG ++ + +A CAATCA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNRNPA 3815 TTGGAGGTGGTGGAAGCTACAATGATTTTGGGAATT-A- -CAACAATCA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNCPA1 482 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 [] \OT1/cmtt/m/n/10 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNRNPA 3861 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNCPA1 531 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 [] \OT1/cmtt/m/n/10 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNRNPA 3910 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNCPA1 580 AAG GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 [] \OT1/cmtt/m/n/10 AAG GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1463--1463 []\OT1/cmtt/m/n/10 HSHNRNPA 3959 AAG<-3962:4251->GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] [35] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1570--1570 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1570--1570 []\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o f_sequence"[] [36] [37] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1598--1598 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 1632--1632 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_MyProteinSW(seqone,seqtwo,mat,-12, -2,NULL);[] Overfull \hbox (127.49588pt too wide) in paragraph at lines 1632--1632 [] \OT1/cmtt/m/n/10 fprintf(stdout,"%d,%d are matched with score %d\n",uni t->i+1,unit->j+1,unit->score);[] [38] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1725--1725 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1725--1725 []\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o f_sequence"[] [39] [40] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1847--1847 []\OT1/cmtt/m/n/10 query type="MySequence*" name="query" field:len="length_of _sequence"[] Overfull \hbox (27.74675pt too wide) in paragraph at lines 1847--1847 []\OT1/cmtt/m/n/10 target type="MySequence*" name="target" field:len="length_o f_sequence"[] [41] Overfull \hbox (258.74474pt too wide) in paragraph at lines 1847--1847 [] \OT1/cmtt/m/n/10 calc="ALPHA_SEQ_SCORE(query,i) + ALPHA_SEQ_SCORE(target,j) + mat_alpha.comp[SEQ_POS(query,i)][SEQ_POS(target,j)]"[] [42] [43] Overfull \hbox (20.54509pt too wide) in paragraph at lines 1909--1910 []\OT1/cmr/m/n/10 The macro Dna-Ma-trix[]Score which is de-fined at the top of the cdna2genomic.dy [44] Overfull \hbox (17.24684pt too wide) in paragraph at lines 1926--1926 [] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,i),GENOMIC_CODON(ta rget,j))"[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1942--1942 [] \OT1/cmtt/m/n/10 Mis-type in argument 3 of DNA\_MAT\_SCORE: wanted [b ase] got [codon][] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1953--1953 [] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,j),GENOMIC_BASE(tar get,j))"[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 1965--1965 [] \OT1/cmtt/m/n/10 For function CDNA\_BASE, you have arguments j and qu ery, which do not[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1965--1965 []\OT1/cmtt/m/n/10 expect to paired directly in a function. This is just a warn ing that[] [45] Overfull \hbox (17.24684pt too wide) in paragraph at lines 2012--2012 [] \OT1/cmtt/m/n/10 throw_warning("Letter %c does not exist in comparison matr ix",one);[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 2012--2012 [] \OT1/cmtt/m/n/10 throw_warning("Letter %c does not exist in comparison matr ix",two);[] [46] [47] Overfull \hbox (74.99634pt too wide) in paragraph at lines 2253--2253 [] \OT1/cmtt/m/n/10 fprintf(stdout,"dbsearch [options] \n");[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 2253--2253 [] \OT1/cmtt/m/n/10 /** add more options here sometime, eg comp matrix and gap penalty*/[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 2253--2253 [] \OT1/cmtt/m/n/10 /** print out dbsearch options. We don't know here what im plementations are[] Overfull \hbox (74.99634pt too wide) in paragraph at lines 2253--2253 [] \OT1/cmtt/m/n/10 either possible or how they are specified. Of course, there is the problem[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 2253--2253 [] \OT1/cmtt/m/n/10 that we could clash our options with the dbsearchimpl options, but that[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 2253--2253 [] \OT1/cmtt/m/n/10 is not too likely, and this makes this program future proof wrt to new[] [48] Overfull \hbox (43.49661pt too wide) in paragraph at lines 2253--2253 [] \OT1/cmtt/m/n/10 * care about which implementation is used, and does not k now either (!)[] [49] Overfull \hbox (106.49606pt too wide) in paragraph at lines 2253--2253 [] \OT1/cmtt/m/n/10 /* 10 means a score cutoff of 10, -1 means don't report on stderr search progress */[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 2253--2253 [] \OT1/cmtt/m/n/10 if( search_ProteinSW(dbsi,out,querydb,prodb,mat,-12,-2) != SEARCH_OK )[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 2253--2253 [] \OT1/cmtt/m/n/10 fatal("Some sort of error in the database search. Dieing ungracefully");[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 2253--2253 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] [50] Overfull \hbox (174.74547pt too wide) in paragraph at lines 2253--2253 [] \OT1/cmtt/m/n/10 fprintf(stdout,"Comparison to %s was %d score\n",out-> ds[i]->target->name,out->ds[i]->score);[] Overfull \hbox (1.49698pt too wide) in paragraph at lines 2253--2253 [] \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta rget);[] Overfull \hbox (69.74638pt too wide) in paragraph at lines 2253--2253 []\OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s",te mp->baseseq->name);[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 2253--2253 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs, mat,-12,-2,NULL);[] Overfull \hbox (95.99615pt too wide) in paragraph at lines 2253--2253 []\OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query->na me,temp->baseseq->name);[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 2253--2253 [] \OT1/cmtt/m/n/10 write_pretty_seq_align(alb,query,temp->baseseq,15,50,s tdout);[] Overfull \hbox (32.9967pt too wide) in paragraph at lines 2261--2261 [] \OT1/cmtt/m/n/10 if( search_ProteinSW(dbsi,out,querydb,prodb,mat,-12,-2) != SEARCH_OK )[] Overfull \hbox (53.99652pt too wide) in paragraph at lines 2261--2261 [] \OT1/cmtt/m/n/10 fatal("Some sort of error in the database search. Dieing ungracefully");[] [51] Overfull \hbox (1.49698pt too wide) in paragraph at lines 2290--2290 [] \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta rget);[] [52] [53] [54] [55] [56] Overfull \hbox (1.32472pt too wide) in paragraph at lines 2526--2532 \OT1/cmr/m/n/10 de-scribed by a "state...endstate" multi-line block. Within eac h "state...endstate" [57] [58] [59] [60] [61] Overfull \hbox (1.75064pt too wide) in paragraph at lines 2770--2774 \OT1/cmr/m/n/10 Dy-na-mite file: for ex-am-ple the fol-low-ing er-ror was made by mistyp-ing ``MATCH'' Overfull \hbox (59.24648pt too wide) in paragraph at lines 2790--2790 [] \OT1/cmtt/m/n/10 In matrix ProteinSW - State MATCH asks for source MA TCH2 but there is[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 2790--2790 [] \OT1/cmtt/m/n/10 Failing simple cross-checks, aborting before calc-li ne parsing[] [62] [63] [64] (./dynamite.aux) LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on dynamite.pdf (64 pages, 217783 bytes). Transcript written on dynamite.log. cd docs && pdflatex wise2.tex This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013/Debian) restricted \write18 enabled. entering extended mode (./wise2.tex LaTeX2e <2011/06/27> Babel <3.9f> and hyphenation patterns for 2 languages loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))) No file wise2.aux. (/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] No file wise2.toc. [2] [3] [4] LaTeX Warning: Reference `genewise_large' on page 5 undefined on input line 108 . LaTeX Warning: Reference `estwise_large' on page 5 undefined on input line 111. Overfull \hbox (11.99689pt too wide) in paragraph at lines 204--204 []\OT1/cmtt/m/n/10 This program is freely distributed under a GPL. See source d irectory[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 204--204 []\OT1/cmtt/m/n/10 Copyright (c) GRL limited: portions of the code are from sep arate copyright[] [5] Overfull \hbox (32.9967pt too wide) in paragraph at lines 204--204 []\OT1/cmtt/m/n/10 Warning: The bits scores is not probablistically correct for single seqs[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 204--204 []\OT1/cmtt/m/n/10 roa1_drome 88 AQKSRPHKIDGRVVEPKRAVPRQ DID[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 204--204 [] \OT1/cmtt/m/n/10 A +RPHK+DGRVVEPKRAV R+ D[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 204--204 [] \OT1/cmtt/m/n/10 AMNARPHKVDGRVVEPKRAVSRE DSQ[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 204--204 []\OT1/cmtt/m/n/10 HSHNRNPA 1867 gaagaccagggagggcaaggtagGTGAGTG Intron 2 TAGgtc[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 204--204 [] \OT1/cmtt/m/n/10 ctacgcaataggttacagctcga<0-----[1936 : 2 083]-0>aca[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 204--204 [] \OT1/cmtt/m/n/10 tgtagacggtaatgaagatccaa tta[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 204--204 []\OT1/cmtt/m/n/10 roa1_drome 114 SPNAGATVKKLFVGALKDDHDEQSIRDYFQHFGNIVDIN IVIDKETGKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 204--204 [] \OT1/cmtt/m/n/10 P A TVKK+FVG +K+D +E +RDYF+ +G I I I+ D+ +GKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 204--204 [] \OT1/cmtt/m/n/10 RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIE IMTDRGSGKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 204--204 []\OT1/cmtt/m/n/10 HSHNRNPA 2093 acggctagaaatgggaaggaggcccagttgctgaaggag aaagcgagaa[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 204--204 [] \OT1/cmtt/m/n/10 gcgcatctaatttggtaaacaaaatgaataaagatatta ttcaggggaa[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 204--204 [] \OT1/cmtt/m/n/10 aatccatgagatttctaactaatcaatttagtaatagta cgtcactcga[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 204--204 []\OT1/cmtt/m/n/10 roa1_drome 163 RGFAFVEFDDYDPVDKVV QKQHQ[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 204--204 [] \OT1/cmtt/m/n/10 RGFAFV FDD+D VDK+V QK H[] [6] Overfull \hbox (22.4968pt too wide) in paragraph at lines 204--204 [] \OT1/cmtt/m/n/10 RGFAFVTFDDHDSVDKIV L:I[att] QKYHT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 204--204 []\OT1/cmtt/m/n/10 HSHNRNPA 2240 agtgtgatggcgtggaagAGTAAGTA Intron 3 TAGTTcatca[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 204--204 [] \OT1/cmtt/m/n/10 ggtcttctaaaactaatt <1-----[2295 : 2387] -1> aaaac[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 204--204 [] \OT1/cmtt/m/n/10 gctctactcctccgtgtc gactt[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 204--204 [] \OT1/cmtt/m/n/10 tagaagatgactcaaatcgcccgag <1-----[2481 : 2793][] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [7] [8] LaTeX Warning: Reference `sec:start_end' on page 9 undefined on input line 295. [9] LaTeX Warning: Reference `half_and_blast' on page 10 undefined on input line 34 4. [10] [11] LaTeX Warning: Reference `genewise_large' on page 12 undefined on input line 45 3. LaTeX Warning: Reference `estwise_large' on page 12 undefined on input line 453 . LaTeX Warning: Reference `compile_pthread' on page 12 undefined on input line 4 64. LaTeX Warning: Reference `half_and_blast' on page 12 undefined on input line 47 1. [12] LaTeX Warning: Reference `half_and_blast' on page 13 undefined on input line 51 1. [13] [14] LaTeX Warning: Reference `running_pthread' on page 15 undefined on input line 6 11. [15] [16] [17] LaTeX Warning: Reference `Figure:genewise21' on page 18 undefined on input line 706. [18] [19] [20] LaTeX Warning: Reference `Figure:genewise623' on page 21 undefined on input lin e 898. [21] Overfull \hbox (2.03789pt too wide) in paragraph at lines 963--966 []\OT1/cmr/m/n/10 Algorithms are named in two parts, \OT1/cmr/m/it/10 descripti ve-word state-number:transition- [22] [23] [24] [25] Overfull \hbox (68.08423pt too wide) in paragraph at lines 1106--1107 []\OT1/cmr/m/n/10 The half-wise pro-tein database, found at ftp://ftp.sanger.ac .uk/pub/birney/wise2/halfwise [26] LaTeX Warning: Reference `sec:commonmode' on page 27 undefined on input line 11 79. [27] LaTeX Warning: Reference `sec:start_end' on page 28 undefined on input line 120 8. [28] Overfull \hbox (42.24687pt too wide) in paragraph at lines 1266--1266 []\OT1/cmtt/m/n/10 pexon [] Overfull \hbox (42.24687pt too wide) in paragraph at lines 1266--1266 []\OT1/cmtt/m/n/10 pexon [] [29] LaTeX Warning: Reference `sec:alg' on page 30 undefined on input line 1274. Overfull \hbox (36.99692pt too wide) in paragraph at lines 1310--1310 []\OT1/cmtt/m/n/10 Bits Query start end Target start end idel s introns[] Overfull \hbox (5.4972pt too wide) in paragraph at lines 1310--1310 []\OT1/cmtt/m/n/10 230.57 roa1_drome 26 347 HSHNRNPA 1386 3963 0 6[] [30] [31] LaTeX Warning: Reference `sec:start_end' on page 32 undefined on input line 137 5. [32] [33] [34] LaTeX Warning: Reference `sec:start_end' on page 35 undefined on input line 146 7. [35] [36] LaTeX Warning: Reference `compile_pthread' on page 37 undefined on input line 1 559. [37] [38] [39] [40] [41] [42] (./wise2.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on wise2.pdf (42 pages, 205926 bytes). Transcript written on wise2.log. cd docs && pdflatex wise2.tex This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013/Debian) restricted \write18 enabled. entering extended mode (./wise2.tex LaTeX2e <2011/06/27> Babel <3.9f> and hyphenation patterns for 2 languages loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/pdftex-def/pdftex.def (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/infwarerr.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ltxcmds.sty)))) (./wise2.aux) (/usr/share/texlive/texmf-dist/tex/context/base/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/pdftexcmds.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifluatex.sty) (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/ifpdf.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvdefinekeys.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/etexcmds.sty))) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./wise2.toc [2]) [3] [4] [5] Overfull \hbox (11.99689pt too wide) in paragraph at lines 204--204 []\OT1/cmtt/m/n/10 This program is freely distributed under a GPL. See source d irectory[] Overfull \hbox (48.74657pt too wide) in paragraph at lines 204--204 []\OT1/cmtt/m/n/10 Copyright (c) GRL limited: portions of the code are from sep arate copyright[] [6] Overfull \hbox (32.9967pt too wide) in paragraph at lines 204--204 []\OT1/cmtt/m/n/10 Warning: The bits scores is not probablistically correct for single seqs[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 204--204 []\OT1/cmtt/m/n/10 roa1_drome 88 AQKSRPHKIDGRVVEPKRAVPRQ DID[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 204--204 [] \OT1/cmtt/m/n/10 A +RPHK+DGRVVEPKRAV R+ D[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 204--204 [] \OT1/cmtt/m/n/10 AMNARPHKVDGRVVEPKRAVSRE DSQ[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 204--204 []\OT1/cmtt/m/n/10 HSHNRNPA 1867 gaagaccagggagggcaaggtagGTGAGTG Intron 2 TAGgtc[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 204--204 [] \OT1/cmtt/m/n/10 ctacgcaataggttacagctcga<0-----[1936 : 2 083]-0>aca[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 204--204 [] \OT1/cmtt/m/n/10 tgtagacggtaatgaagatccaa tta[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 204--204 []\OT1/cmtt/m/n/10 roa1_drome 114 SPNAGATVKKLFVGALKDDHDEQSIRDYFQHFGNIVDIN IVIDKETGKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 204--204 [] \OT1/cmtt/m/n/10 P A TVKK+FVG +K+D +E +RDYF+ +G I I I+ D+ +GKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 204--204 [] \OT1/cmtt/m/n/10 RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIE IMTDRGSGKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 204--204 []\OT1/cmtt/m/n/10 HSHNRNPA 2093 acggctagaaatgggaaggaggcccagttgctgaaggag aaagcgagaa[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 204--204 [] \OT1/cmtt/m/n/10 gcgcatctaatttggtaaacaaaatgaataaagatatta ttcaggggaa[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 204--204 [] \OT1/cmtt/m/n/10 aatccatgagatttctaactaatcaatttagtaatagta cgtcactcga[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 204--204 []\OT1/cmtt/m/n/10 roa1_drome 163 RGFAFVEFDDYDPVDKVV QKQHQ[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 204--204 [] \OT1/cmtt/m/n/10 RGFAFV FDD+D VDK+V QK H[] [7] Overfull \hbox (22.4968pt too wide) in paragraph at lines 204--204 [] \OT1/cmtt/m/n/10 RGFAFVTFDDHDSVDKIV L:I[att] QKYHT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 204--204 []\OT1/cmtt/m/n/10 HSHNRNPA 2240 agtgtgatggcgtggaagAGTAAGTA Intron 3 TAGTTcatca[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 204--204 [] \OT1/cmtt/m/n/10 ggtcttctaaaactaatt <1-----[2295 : 2387] -1> aaaac[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 204--204 [] \OT1/cmtt/m/n/10 gctctactcctccgtgtc gactt[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 204--204 [] \OT1/cmtt/m/n/10 tagaagatgactcaaatcgcccgag <1-----[2481 : 2793][] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] LaTeX Warning: Reference `Figure:genewise21' on page 19 undefined on input line 706. [19] [20] [21] [22] Overfull \hbox (2.03789pt too wide) in paragraph at lines 963--966 []\OT1/cmr/m/n/10 Algorithms are named in two parts, \OT1/cmr/m/it/10 descripti ve-word state-number:transition- [23] [24] [25] [26] Overfull \hbox (68.08423pt too wide) in paragraph at lines 1106--1107 []\OT1/cmr/m/n/10 The half-wise pro-tein database, found at ftp://ftp.sanger.ac .uk/pub/birney/wise2/halfwise [27] [28] [29] Overfull \hbox (42.24687pt too wide) in paragraph at lines 1266--1266 []\OT1/cmtt/m/n/10 pexon [] Overfull \hbox (42.24687pt too wide) in paragraph at lines 1266--1266 []\OT1/cmtt/m/n/10 pexon [] [30] Overfull \hbox (36.99692pt too wide) in paragraph at lines 1310--1310 []\OT1/cmtt/m/n/10 Bits Query start end Target start end idel s introns[] Overfull \hbox (5.4972pt too wide) in paragraph at lines 1310--1310 []\OT1/cmtt/m/n/10 230.57 roa1_drome 26 347 HSHNRNPA 1386 3963 0 6[] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] (./wise2.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information) Output written on wise2.pdf (43 pages, 208445 bytes). Transcript written on wise2.log. cd docs && hevea api.tex ./api.tex:231: Warning: Undefined label: 'object_GeneFrequency' ./api.tex:234: Warning: Undefined label: 'module_gwrap' ./api.tex:235: Warning: Undefined label: 'module_gwrap' ./api.tex:236: Warning: Undefined label: 'module_gwrap' ./api.tex:237: Warning: Undefined label: 'module_gwrap' ./api.tex:387: Warning: Undefined label: 'module_gwrap' ./api.tex:424: Warning: Undefined label: 'module_codonmat' ./api.tex:433: Warning: Undefined label: 'module_dbimpl' ./api.tex:852: Warning: Application of '\'' on 'd' failed ./api.tex:852: Warning: Application of '\'' on 'd' failed ./api.tex:1709: Warning: Application of '\'' on 'f' failed ./api.tex:1709: Warning: Application of '\'' on '[' failed ./api.tex:1730: Warning: Application of '\'' on 'f' failed ./api.tex:1730: Warning: Application of '\'' on '[' failed ./api.tex:1840: Warning: Application of '\'' on ',' failed ./api.tex:1993: Warning: Application of '\'' on 't' failed ./api.tex:1995: Warning: Application of '\'' on 'b' failed ./api.tex:1997: Warning: Application of '\'' on 'b' failed ./api.tex:3006: Warning: Application of '\'' on 't' failed ./api.tex:3024: Warning: Application of '\'' on 't' failed ./api.tex:3246: Warning: Application of '\'' on '.' failed ./api.tex:3805: Warning: Application of '\'' on 'b' failed ./api.tex:4211: Warning: Application of '\'' on 'h' failed ./api.tex:4211: Warning: Application of '\'' on 't' failed ./api.tex:5799: Warning: Application of '\'' on '.' failed cd docs && hevea api.tex ./api.tex:231: Warning: Undefined label: 'object_GeneFrequency' ./api.tex:234: Warning: Undefined label: 'module_gwrap' ./api.tex:235: Warning: Undefined label: 'module_gwrap' ./api.tex:236: Warning: Undefined label: 'module_gwrap' ./api.tex:237: Warning: Undefined label: 'module_gwrap' ./api.tex:387: Warning: Undefined label: 'module_gwrap' ./api.tex:424: Warning: Undefined label: 'module_codonmat' ./api.tex:433: Warning: Undefined label: 'module_dbimpl' ./api.tex:852: Warning: Application of '\'' on 'd' failed ./api.tex:852: Warning: Application of '\'' on 'd' failed ./api.tex:1709: Warning: Application of '\'' on 'f' failed ./api.tex:1709: Warning: Application of '\'' on '[' failed ./api.tex:1730: Warning: Application of '\'' on 'f' failed ./api.tex:1730: Warning: Application of '\'' on '[' failed ./api.tex:1840: Warning: Application of '\'' on ',' failed ./api.tex:1993: Warning: Application of '\'' on 't' failed ./api.tex:1995: Warning: Application of '\'' on 'b' failed ./api.tex:1997: Warning: Application of '\'' on 'b' failed ./api.tex:3006: Warning: Application of '\'' on 't' failed ./api.tex:3024: Warning: Application of '\'' on 't' failed ./api.tex:3246: Warning: Application of '\'' on '.' failed ./api.tex:3805: Warning: Application of '\'' on 'b' failed ./api.tex:4211: Warning: Application of '\'' on 'h' failed ./api.tex:4211: Warning: Application of '\'' on 't' failed ./api.tex:5799: Warning: Application of '\'' on '.' failed cd docs && hevea dynamite.tex ./dynamite.tex:2616: Warning: Command not found: \+ ./dynamite.tex:2616: Warning: Command not found: \* ./dynamite.tex:2617: Warning: Command not found: \* ./dynamite.tex:2754: Warning: Application of '\"' on ')' failed ./dynamite.tex:2754: Warning: Application of '\"' on ')' failed cd docs && hevea dynamite.tex ./dynamite.tex:2616: Warning: Command not found: \+ ./dynamite.tex:2616: Warning: Command not found: \* ./dynamite.tex:2617: Warning: Command not found: \* ./dynamite.tex:2754: Warning: Application of '\"' on ')' failed ./dynamite.tex:2754: Warning: Application of '\"' on ')' failed cd docs && hevea wise2.tex ./wise2.tex:239: Warning: \hbox ./wise2.tex:241: Warning: \hbox ./wise2.tex:243: Warning: \hbox ./wise2.tex:245: Warning: \hbox ./wise2.tex:247: Warning: \hbox ./wise2.tex:249: Warning: \hbox ./wise2.tex:251: Warning: \hbox ./wise2.tex:253: Warning: \hbox ./wise2.tex:261: Warning: \hbox ./wise2.tex:263: Warning: \hbox ./wise2.tex:265: Warning: \hbox ./wise2.tex:267: Warning: \hbox ./wise2.tex:269: Warning: \hbox ./wise2.tex:271: Warning: \hbox ./wise2.tex:273: Warning: \hbox ./wise2.tex:275: Warning: \hbox ./wise2.tex:706: Warning: Undefined label: 'Figure:genewise21' ./wise2.tex:710: Warning: Command not found: \leavevmode ./wise2.tex:902: Warning: Command not found: \leavevmode cd docs && hevea wise2.tex ./wise2.tex:239: Warning: \hbox ./wise2.tex:241: Warning: \hbox ./wise2.tex:243: Warning: \hbox ./wise2.tex:245: Warning: \hbox ./wise2.tex:247: Warning: \hbox ./wise2.tex:249: Warning: \hbox ./wise2.tex:251: Warning: \hbox ./wise2.tex:253: Warning: \hbox ./wise2.tex:261: Warning: \hbox ./wise2.tex:263: Warning: \hbox ./wise2.tex:265: Warning: \hbox ./wise2.tex:267: Warning: \hbox ./wise2.tex:269: Warning: \hbox ./wise2.tex:271: Warning: \hbox ./wise2.tex:273: Warning: \hbox ./wise2.tex:275: Warning: \hbox ./wise2.tex:706: Warning: Undefined label: 'Figure:genewise21' ./wise2.tex:710: Warning: Command not found: \leavevmode ./wise2.tex:902: Warning: Command not found: \leavevmode mkdir -p docs/api mkdir -p docs/dynamite mkdir -p docs/wise2 mv docs/api.html docs/api mv docs/dynamite.html docs/dynamite mv docs/wise2.html docs/wise2 dh_auto_build make[1]: Leaving directory `/build/buildd/wise-2.4.1' dh_auto_test /usr/bin/fakeroot debian/rules binary dh binary dh_testroot dh_prep rm -f debian/wise.substvars rm -f debian/wise.*.debhelper rm -rf debian/wise/ rm -f debian/wise-doc.substvars rm -f debian/wise-doc.*.debhelper rm -rf debian/wise-doc/ rm -f debian/wise-data.substvars rm -f debian/wise-data.*.debhelper rm -rf debian/wise-data/ dh_installdirs install -d debian/wise install -d debian/wise/usr/bin install -d debian/wise-doc install -d debian/wise-data install -d debian/wise-data/usr/share/wise dh_auto_install dh_install cp -a ./src/bin/dba debian/wise/usr/bin/ cp -a ./src/bin/dnal debian/wise/usr/bin/ cp -a ./src/bin/estwise debian/wise/usr/bin/ cp -a ./src/bin/estwisedb debian/wise/usr/bin/ cp -a ./src/bin/genewise debian/wise/usr/bin/ cp -a ./src/bin/genewisedb debian/wise/usr/bin/ cp -a ./src/bin/promoterwise debian/wise/usr/bin/ cp -a ./src/bin/psw debian/wise/usr/bin/ cp -a ./src/bin/pswdb debian/wise/usr/bin/ cp -a ./src/bin/scanwise debian/wise/usr/bin/ cp -a ./src/bin/scanwise_server debian/wise/usr/bin/ cp -a ./src/models/genomewise debian/wise/usr/bin/ cp -a ./wisecfg/aa.rnd debian/wise-data/usr/share/wise/ cp -a ./wisecfg/BLOSUM30.bla debian/wise-data/usr/share/wise/ cp -a ./wisecfg/BLOSUM45.bla debian/wise-data/usr/share/wise/ cp -a ./wisecfg/BLOSUM62.bla debian/wise-data/usr/share/wise/ cp -a ./wisecfg/BLOSUM80.bla debian/wise-data/usr/share/wise/ cp -a ./wisecfg/cb.tmf debian/wise-data/usr/share/wise/ cp -a ./wisecfg/codon.martian debian/wise-data/usr/share/wise/ cp -a ./wisecfg/codon.table debian/wise-data/usr/share/wise/ cp -a ./wisecfg/gene.stat debian/wise-data/usr/share/wise/ cp -a ./wisecfg/gon120.bla debian/wise-data/usr/share/wise/ cp -a ./wisecfg/gon160.bla debian/wise-data/usr/share/wise/ cp -a ./wisecfg/gon200.bla debian/wise-data/usr/share/wise/ cp -a ./wisecfg/gon250.bla debian/wise-data/usr/share/wise/ cp -a ./wisecfg/gon350.bla debian/wise-data/usr/share/wise/ cp -a ./wisecfg/human.gf debian/wise-data/usr/share/wise/ cp -a ./wisecfg/human.gp debian/wise-data/usr/share/wise/ cp -a ./wisecfg/human.stats debian/wise-data/usr/share/wise/ cp -a ./wisecfg/idenity.bla debian/wise-data/usr/share/wise/ cp -a ./wisecfg/methods debian/wise-data/usr/share/wise/ cp -a ./wisecfg/pb.gf debian/wise-data/usr/share/wise/ cp -a ./wisecfg/pombe.gf debian/wise-data/usr/share/wise/ cp -a ./wisecfg/tm.pri debian/wise-data/usr/share/wise/ cp -a ./wisecfg/wag55 debian/wise-data/usr/share/wise/ cp -a ./wisecfg/wag65 debian/wise-data/usr/share/wise/ cp -a ./wisecfg/wag75 debian/wise-data/usr/share/wise/ cp -a ./wisecfg/wag85 debian/wise-data/usr/share/wise/ cp -a ./wisecfg/wise.2 debian/wise-data/usr/share/wise/ cp -a ./wisecfg/wise.per debian/wise-data/usr/share/wise/ cp -a ./wisecfg/worm.gf debian/wise-data/usr/share/wise/ dh_installdocs install -g 0 -o 0 -d debian/wise/usr/share/doc/wise cp -a README debian/wise/usr/share/doc/wise chown -R 0:0 debian/wise/usr/share/doc chmod -R go=rX debian/wise/usr/share/doc chmod -R u\+rw debian/wise/usr/share/doc install -g 0 -o 0 -m 644 -p debian/README.Debian debian/wise/usr/share/doc/wise/README.Debian install -g 0 -o 0 -m 644 -p debian/copyright debian/wise/usr/share/doc/wise/copyright install -g 0 -o 0 -d debian/wise-doc/usr/share/doc/wise-doc cp -a docs/api.pdf debian/wise-doc/usr/share/doc/wise-doc cp -a docs/dynamite.pdf debian/wise-doc/usr/share/doc/wise-doc cp -a docs/wise2.pdf debian/wise-doc/usr/share/doc/wise-doc cd 'docs/api/..' && find 'api' \( -type f -or -type l \) -and ! -empty -exec cp --parents -dp {} /build/buildd/wise-2.4.1/debian/wise-doc/usr/share/doc/wise-doc \; cd 'docs/dynamite/..' && find 'dynamite' \( -type f -or -type l \) -and ! -empty -exec cp --parents -dp {} /build/buildd/wise-2.4.1/debian/wise-doc/usr/share/doc/wise-doc \; cd 'docs/wise2/..' && find 'wise2' \( -type f -or -type l \) -and ! -empty -exec cp --parents -dp {} /build/buildd/wise-2.4.1/debian/wise-doc/usr/share/doc/wise-doc \; chown -R 0:0 debian/wise-doc/usr/share/doc chmod -R go=rX debian/wise-doc/usr/share/doc chmod -R u\+rw debian/wise-doc/usr/share/doc install -g 0 -o 0 -m 644 -p debian/copyright debian/wise-doc/usr/share/doc/wise-doc/copyright install -g 0 -o 0 -d debian/wise-doc/usr/share/doc-base/ install -g 0 -o 0 -m644 -p debian/wise-doc.doc-base.api debian/wise-doc/usr/share/doc-base/wise-api install -g 0 -o 0 -m644 -p debian/wise-doc.doc-base.wise debian/wise-doc/usr/share/doc-base/wise install -g 0 -o 0 -m644 -p debian/wise-doc.doc-base.dynamite debian/wise-doc/usr/share/doc-base/wise-dynamite install -g 0 -o 0 -d debian/wise-data/usr/share/doc/wise-data install -g 0 -o 0 -m 644 -p debian/copyright debian/wise-data/usr/share/doc/wise-data/copyright dh_installchangelogs install -o 0 -g 0 -p -m644 debian/changelog debian/wise/usr/share/doc/wise/changelog.Debian install -o 0 -g 0 -p -m644 debian/changelog debian/wise-doc/usr/share/doc/wise-doc/changelog.Debian install -o 0 -g 0 -p -m644 debian/changelog debian/wise-data/usr/share/doc/wise-data/changelog.Debian dh_installman install -d debian/wise/usr/share/man/man1/ install -p -m644 debian/manpages.d/dba.1 debian/wise/usr/share/man/man1/dba.1 install -p -m644 debian/manpages.d/dnal.1 debian/wise/usr/share/man/man1/dnal.1 install -p -m644 debian/manpages.d/estwise.1 debian/wise/usr/share/man/man1/estwise.1 install -p -m644 debian/manpages.d/estwisedb.1 debian/wise/usr/share/man/man1/estwisedb.1 install -p -m644 debian/manpages.d/genewise.1 debian/wise/usr/share/man/man1/genewise.1 install -p -m644 debian/manpages.d/genewisedb.1 debian/wise/usr/share/man/man1/genewisedb.1 install -p -m644 debian/manpages.d/genomewise.1 debian/wise/usr/share/man/man1/genomewise.1 install -p -m644 debian/manpages.d/promoterwise.1 debian/wise/usr/share/man/man1/promoterwise.1 install -p -m644 debian/manpages.d/psw.1 debian/wise/usr/share/man/man1/psw.1 install -p -m644 debian/manpages.d/pswdb.1 debian/wise/usr/share/man/man1/pswdb.1 install -p -m644 debian/manpages.d/scanwise.1 debian/wise/usr/share/man/man1/scanwise.1 install -p -m644 debian/manpages.d/scanwise_server.1 debian/wise/usr/share/man/man1/scanwise_server.1 man --recode UTF-8 ./estwisedb\.1 > estwisedb\.1\.new chmod 644 estwisedb.1.new mv -f estwisedb.1.new estwisedb.1 man --recode UTF-8 ./genewisedb\.1 > genewisedb\.1\.new chmod 644 genewisedb.1.new mv -f genewisedb.1.new genewisedb.1 man --recode UTF-8 ./genomewise\.1 > genomewise\.1\.new chmod 644 genomewise.1.new mv -f genomewise.1.new genomewise.1 man --recode UTF-8 ./pswdb\.1 > pswdb\.1\.new chmod 644 pswdb.1.new mv -f pswdb.1.new pswdb.1 man --recode UTF-8 ./promoterwise\.1 > promoterwise\.1\.new chmod 644 promoterwise.1.new mv -f promoterwise.1.new promoterwise.1 man --recode UTF-8 ./scanwise_server\.1 > scanwise_server\.1\.new chmod 644 scanwise_server.1.new mv -f scanwise_server.1.new scanwise_server.1 man --recode UTF-8 ./scanwise\.1 > scanwise\.1\.new chmod 644 scanwise.1.new mv -f scanwise.1.new scanwise.1 man --recode UTF-8 ./estwise\.1 > estwise\.1\.new chmod 644 estwise.1.new mv -f estwise.1.new estwise.1 man --recode UTF-8 ./psw\.1 > psw\.1\.new chmod 644 psw.1.new mv -f psw.1.new psw.1 man --recode UTF-8 ./dnal\.1 > dnal\.1\.new chmod 644 dnal.1.new mv -f dnal.1.new dnal.1 man --recode UTF-8 ./genewise\.1 > genewise\.1\.new chmod 644 genewise.1.new mv -f genewise.1.new genewise.1 man --recode UTF-8 ./dba\.1 > dba\.1\.new chmod 644 dba.1.new mv -f dba.1.new dba.1 dh_perl dh_link dh_compress cd debian/wise chmod a-x usr/share/man/man1/estwisedb.1 usr/share/man/man1/genewisedb.1 usr/share/man/man1/genomewise.1 usr/share/man/man1/pswdb.1 usr/share/man/man1/promoterwise.1 usr/share/man/man1/scanwise_server.1 usr/share/man/man1/scanwise.1 usr/share/man/man1/estwise.1 usr/share/man/man1/psw.1 usr/share/man/man1/dnal.1 usr/share/man/man1/genewise.1 usr/share/man/man1/dba.1 usr/share/doc/wise/changelog.Debian gzip -9nf usr/share/man/man1/estwisedb.1 usr/share/man/man1/genewisedb.1 usr/share/man/man1/genomewise.1 usr/share/man/man1/pswdb.1 usr/share/man/man1/promoterwise.1 usr/share/man/man1/scanwise_server.1 usr/share/man/man1/scanwise.1 usr/share/man/man1/estwise.1 usr/share/man/man1/psw.1 usr/share/man/man1/dnal.1 usr/share/man/man1/genewise.1 usr/share/man/man1/dba.1 usr/share/doc/wise/changelog.Debian cd '/build/buildd/wise-2.4.1' cd debian/wise-doc chmod a-x usr/share/doc/wise-doc/wise2.pdf usr/share/doc/wise-doc/api.pdf usr/share/doc/wise-doc/dynamite.pdf usr/share/doc/wise-doc/changelog.Debian gzip -9nf usr/share/doc/wise-doc/wise2.pdf usr/share/doc/wise-doc/api.pdf usr/share/doc/wise-doc/dynamite.pdf usr/share/doc/wise-doc/changelog.Debian cd '/build/buildd/wise-2.4.1' cd debian/wise-data chmod a-x usr/share/doc/wise-data/changelog.Debian gzip -9nf usr/share/doc/wise-data/changelog.Debian cd '/build/buildd/wise-2.4.1' dh_fixperms find debian/wise -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/wise ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/wise/usr/share/doc -type f ! -regex 'debian/wise/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644 find debian/wise/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755 find debian/wise/usr/share/man debian/wise/usr/man/ debian/wise/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/wise -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644 find debian/wise/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/wise/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/wise -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644 find debian/wise/usr/lib/perl5 debian/wise/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X find debian/wise/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x find debian/wise/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w find debian/wise-doc -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/wise-doc ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/wise-doc/usr/share/doc -type f ! -regex 'debian/wise-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644 find debian/wise-doc/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755 find debian/wise-doc/usr/share/man debian/wise-doc/usr/man/ debian/wise-doc/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/wise-doc -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644 find debian/wise-doc/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/wise-doc/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/wise-doc -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644 find debian/wise-doc/usr/lib/perl5 debian/wise-doc/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X find debian/wise-doc/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w find debian/wise-data -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/wise-data ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/wise-data/usr/share/doc -type f ! -regex 'debian/wise-data/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644 find debian/wise-data/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755 find debian/wise-data/usr/share/man debian/wise-data/usr/man/ debian/wise-data/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/wise-data -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644 find debian/wise-data/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/wise-data/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/wise-data -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644 find debian/wise-data/usr/lib/perl5 debian/wise-data/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X find debian/wise-data/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w dh_strip dh_strip debug symbol extraction: all non-arch-all packages for this build platform i386: wise dh_strip debug symbol extraction: packages to act on: wise dh_strip debug symbol extraction: ignored packages: dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-deb: building package `wise-dbgsym' in `../wise-dbgsym_2.4.1-14_i386.ddeb'. strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/pswdb strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/estwisedb strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/scanwise_server strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/psw strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/promoterwise strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/dba strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genomewise strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/dnal strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genewise strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/estwise strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/scanwise strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genewisedb dh_makeshlibs rm -f debian/wise/DEBIAN/shlibs rm -f debian/wise-doc/DEBIAN/shlibs rm -f debian/wise-data/DEBIAN/shlibs dh_shlibdeps install -o 0 -g 0 -d debian/wise/DEBIAN dpkg-shlibdeps -Tdebian/wise.substvars debian/wise/usr/bin/pswdb debian/wise/usr/bin/estwisedb debian/wise/usr/bin/scanwise_server debian/wise/usr/bin/psw debian/wise/usr/bin/promoterwise debian/wise/usr/bin/dba debian/wise/usr/bin/genomewise debian/wise/usr/bin/dnal debian/wise/usr/bin/genewise debian/wise/usr/bin/estwise debian/wise/usr/bin/scanwise debian/wise/usr/bin/genewisedb install -o 0 -g 0 -d debian/wise-doc/DEBIAN install -o 0 -g 0 -d debian/wise-data/DEBIAN dh_installdeb dh_gencontrol echo misc:Depends= >> debian/wise.substvars dpkg-gencontrol -pwise -ldebian/changelog -Tdebian/wise.substvars -Pdebian/wise dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe chmod 644 debian/wise/DEBIAN/control chown 0:0 debian/wise/DEBIAN/control echo misc:Depends= >> debian/wise-doc.substvars dpkg-gencontrol -pwise-doc -ldebian/changelog -Tdebian/wise-doc.substvars -Pdebian/wise-doc dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe chmod 644 debian/wise-doc/DEBIAN/control chown 0:0 debian/wise-doc/DEBIAN/control echo misc:Depends= >> debian/wise-data.substvars dpkg-gencontrol -pwise-data -ldebian/changelog -Tdebian/wise-data.substvars -Pdebian/wise-data dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe chmod 644 debian/wise-data/DEBIAN/control chown 0:0 debian/wise-data/DEBIAN/control dh_md5sums (cd debian/wise >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null chmod 644 debian/wise/DEBIAN/md5sums chown 0:0 debian/wise/DEBIAN/md5sums (cd debian/wise-doc >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null chmod 644 debian/wise-doc/DEBIAN/md5sums chown 0:0 debian/wise-doc/DEBIAN/md5sums (cd debian/wise-data >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null chmod 644 debian/wise-data/DEBIAN/md5sums chown 0:0 debian/wise-data/DEBIAN/md5sums debian/rules override_dh_builddeb make[1]: Entering directory `/build/buildd/wise-2.4.1' dh_builddeb -- -Z xz dpkg-deb -Z xz --build debian/wise .. INFO: pkgstriptranslations version 118 pkgstriptranslations: processing wise (in debian/wise); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/wise/DEBIAN/control, package wise, directory debian/wise Skipping arch: any to arch: all dependency to wise-data pkgstripfiles: Truncating usr/share/doc/wise/changelog.Debian.gz to topmost ten records pkgstripfiles: PNG optimization for package wise took 0 s dpkg-deb: warning: 'debian/wise/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `wise' in `../wise_2.4.1-14_i386.deb'. dpkg-deb -Z xz --build debian/wise-doc .. INFO: pkgstriptranslations version 118 pkgstriptranslations: processing wise-doc (in debian/wise-doc); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/wise-doc/DEBIAN/control, package wise-doc, directory debian/wise-doc pkgstripfiles: Truncating usr/share/doc/wise-doc/changelog.Debian.gz to topmost ten records pkgstripfiles: Disabled PNG optimization for -doc package wise-doc (to save build time) dpkg-deb: warning: 'debian/wise-doc/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `wise-doc' in `../wise-doc_2.4.1-14_all.deb'. dpkg-deb -Z xz --build debian/wise-data .. INFO: pkgstriptranslations version 118 pkgstriptranslations: processing wise-data (in debian/wise-data); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/wise-data/DEBIAN/control, package wise-data, directory debian/wise-data pkgstripfiles: Truncating usr/share/doc/wise-data/changelog.Debian.gz to topmost ten records pkgstripfiles: PNG optimization for package wise-data took 0 s dpkg-deb: warning: 'debian/wise-data/DEBIAN/control' contains user-defined field 'Original-Maintainer' dpkg-deb: warning: ignoring 1 warning about the control file(s) dpkg-deb: building package `wise-data' in `../wise-data_2.4.1-14_all.deb'. make[1]: Leaving directory `/build/buildd/wise-2.4.1' dpkg-genchanges -b -mUbuntu/amd64 Build Daemon >../wise_2.4.1-14_i386.changes dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build wise-2.4.1 dpkg-buildpackage: binary only upload (no source included) ****************************************************************************** Build finished at 20130717-1053 Publishing debug debs. chroot-autobuild/build/buildd/wise_2.4.1-14_i386.deb: new debian package, version 2.0. size 900384 bytes: control archive= 1972 bytes. 1831 bytes, 35 lines control 1675 bytes, 28 lines md5sums Package: wise Version: 2.4.1-14 Architecture: i386 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 9664 Pre-Depends: dpkg (>= 1.15.6~) Depends: libc6 (>= 2.7), libglib2.0-0 (>= 2.12.0), wise-data (= 2.4.1-14) Suggests: wise-doc (= 2.4.1-14) Section: science Priority: optional Homepage: http://www.ebi.ac.uk/~birney/wise2/ Description: comparison of biopolymers, commonly DNA and protein sequences Wise2 is a package focused on comparisons of biopolymers, commonly DNA and protein sequences. There are many other packages which do this, probably the best known being BLAST package (from NCBI) and the Fasta package (from Bill Pearson). There are other packages, such as the HMMER package (Sean Eddy) or SAM package (UC Santa Cruz) focused on hidden Markov models (HMMs) of biopolymers. . Wise2's particular forte is the comparison of DNA sequence at the level of its protein translation. This comparison allows the simultaneous prediction of say gene structure with homology based alignment. . Wise2 also contains other algorithms, such as the venerable Smith-Waterman algorithm, or more modern ones such as Stephen Altschul's generalised gap penalties, or even experimental ones developed in house, such as dba. The development of these algorithms is due to the ease of developing such algorithms in the environment used by Wise2. . Wise2 has also been written with an eye for reuse and maintainability. Although it is a pure C package you can access its functionality directly in Perl. Parts of the package (or the entire package) can be used by other C or C++ programs without namespace clashes as all externally linked variables have the unique identifier Wise2 prepended. chroot-autobuild/build/buildd/wise-doc_2.4.1-14_all.deb: new debian package, version 2.0. size 817576 bytes: control archive= 899 bytes. 603 bytes, 15 lines control 766 bytes, 11 lines md5sums Package: wise-doc Source: wise Version: 2.4.1-14 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1310 Pre-Depends: dpkg (>= 1.15.6~) Recommends: wise (= 2.4.1-14), xpdf-reader | pdf-viewer Section: doc Priority: optional Homepage: http://www.ebi.ac.uk/~birney/wise2/ Description: documentation for the wise package This package contains the documentation for Wise2, a package focused on comparisons of biopolymers, commonly DNA and protein sequences. chroot-autobuild/build/buildd/wise-data_2.4.1-14_all.deb: new debian package, version 2.0. size 33910 bytes: control archive= 1397 bytes. 567 bytes, 15 lines control 1844 bytes, 31 lines md5sums Package: wise-data Source: wise Version: 2.4.1-14 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 160 Pre-Depends: dpkg (>= 1.15.6~) Recommends: wise (= 2.4.1-14) Section: doc Priority: optional Homepage: http://www.ebi.ac.uk/~birney/wise2/ Description: data files for the wise package This package contains data files for Wise2, a package focused on comparisons of biopolymers, commonly DNA and protein sequences. chroot-autobuild/build/buildd/wise_2.4.1-14_i386.deb: drwxr-xr-x root/root 0 2013-07-17 10:52 ./ drwxr-xr-x root/root 0 2013-07-17 10:52 ./usr/ drwxr-xr-x root/root 0 2013-07-17 10:52 ./usr/share/ drwxr-xr-x root/root 0 2013-07-17 10:52 ./usr/share/man/ drwxr-xr-x root/root 0 2013-07-17 10:52 ./usr/share/man/man1/ -rw-r--r-- root/root 619 2013-07-17 10:52 ./usr/share/man/man1/genewisedb.1.gz -rw-r--r-- root/root 869 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./usr/bin/scanwise -rwxr-xr-x root/root 1855028 2013-07-17 10:52 ./usr/bin/genewisedb chroot-autobuild/build/buildd/wise-doc_2.4.1-14_all.deb: drwxr-xr-x root/root 0 2013-07-17 10:52 ./ drwxr-xr-x root/root 0 2013-07-17 10:52 ./usr/ drwxr-xr-x root/root 0 2013-07-17 10:52 ./usr/share/ drwxr-xr-x root/root 0 2013-07-17 10:52 ./usr/share/doc/ drwxr-xr-x root/root 0 2013-07-17 10:52 ./usr/share/doc/wise-doc/ -rw-r--r-- root/root 309534 2013-07-17 10:52 ./usr/share/doc/wise-doc/api.pdf.gz drwxr-xr-x root/root 0 2013-07-17 10:52 ./usr/share/doc/wise-doc/wise2/ -rw-r--r-- root/root 118201 2013-07-17 10:52 ./usr/share/doc/wise-doc/wise2/wise2.html -rw-r--r-- root/root 4219 2012-03-30 10:07 ./usr/share/doc/wise-doc/copyright drwxr-xr-x root/root 0 2013-07-17 10:52 ./usr/share/doc/wise-doc/api/ -rw-r--r-- root/root 339713 2013-07-17 10:52 ./usr/share/doc/wise-doc/api/api.html -rw-r--r-- root/root 212660 2013-07-17 10:52 ./usr/share/doc/wise-doc/dynamite.pdf.gz drwxr-xr-x root/root 0 2013-07-17 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-rw-r--r-- root/root 4219 2012-03-30 10:07 ./usr/share/doc/wise-data/copyright -rw-r--r-- root/root 1356 2013-07-17 10:53 ./usr/share/doc/wise-data/changelog.Debian.gz wise_2.4.1-14_i386.changes: Format: 1.8 Date: Mon, 15 Jul 2013 18:22:15 +0200 Source: wise Binary: wise wise-doc wise-data Architecture: i386 all Version: 2.4.1-14 Distribution: saucy-proposed Urgency: low Maintainer: Ubuntu/amd64 Build Daemon Changed-By: Philipp Benner Description: wise - comparison of biopolymers, commonly DNA and protein sequences wise-data - data files for the wise package wise-doc - documentation for the wise package Closes: 716983 Changes: wise (2.4.1-14) unstable; urgency=low . * Fixed FTBFS bug (Closes: #716983). Checksums-Sha1: 2558ab3f6b2293ab2ae4a3f8584e9a1ed5e24f25 900384 wise_2.4.1-14_i386.deb 8ec5b88e7d744205d82493c2bc5cbd6aa870f958 817576 wise-doc_2.4.1-14_all.deb 3304b0f5066f71aa3e8144ef1b7d1b491b050485 33910 wise-data_2.4.1-14_all.deb Checksums-Sha256: 9f5b9f6156413f2b31c3ef5627dc79145c7bed0b9afa16835e6c40ec19a68911 900384 wise_2.4.1-14_i386.deb 51b3e100d5d1993455dd60ff057dbdf5802f8c2d5ae30bc57c1fc21737568b9e 817576 wise-doc_2.4.1-14_all.deb a5b96bc804578a56bb81131d0af7d9810044ead3481fa5ebadc36f7bac46c726 33910 wise-data_2.4.1-14_all.deb Files: 6e86e7ac39bc9b4d3b7958d7f713c3ab 900384 science optional wise_2.4.1-14_i386.deb 4cbfeb04d4524d711c19a96161b2d860 817576 doc optional wise-doc_2.4.1-14_all.deb 8d5246a73862f242460a52104ceadbf8 33910 doc optional wise-data_2.4.1-14_all.deb ****************************************************************************** Built successfully ****************************************************************************** Finished at 20130717-1053 Build needed 00:03:09, 117560k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['/usr/share/launchpad-buildd/slavebin/scan-for-processes', '5d2a6dc963d721587589db108f03484968e1ef24'] Scanning for processes to kill in build /home/buildd/build-5d2a6dc963d721587589db108f03484968e1ef24/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', '5d2a6dc963d721587589db108f03484968e1ef24'] Unmounting chroot for build 5d2a6dc963d721587589db108f03484968e1ef24... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', '5d2a6dc963d721587589db108f03484968e1ef24'] Removing build 5d2a6dc963d721587589db108f03484968e1ef24