RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux kapok 3.2.0-58-generic #88-Ubuntu SMP Tue Dec 3 17:37:58 UTC 2013 x86_64 Buildd toolchain package versions: launchpad-buildd_125 python-lpbuildd_125 bzr_2.5.1-0ubuntu2 dpkg-dev_1.16.1.2ubuntu7.5. Syncing the system clock with the buildd NTP service... 25 Oct 23:44:24 ntpdate[21493]: adjust time server 10.211.37.1 offset 0.000050 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-6502313', '/home/buildd/filecache-default/a665269cbd0fd566602516993cd02903b7df1cae'] Unpacking chroot for build PACKAGEBUILD-6502313 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-6502313'] Mounting chroot for build PACKAGEBUILD-6502313 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-6502313', 'deb http://ftpmaster.internal/ubuntu vivid main universe', 'deb http://ftpmaster.internal/ubuntu vivid-security main universe', 'deb http://ftpmaster.internal/ubuntu vivid-updates main universe', 'deb http://ftpmaster.internal/ubuntu vivid-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-6502313 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-6502313', 'amd64'] Updating debian chroot for build PACKAGEBUILD-6502313 Ign http://archive-team.internal vivid InRelease Ign http://ftpmaster.internal vivid InRelease Ign http://archive-team.internal vivid Release.gpg Ign http://ftpmaster.internal vivid-security InRelease Get:1 http://archive-team.internal vivid Release [728 B] Ign http://ftpmaster.internal vivid-updates InRelease Ign http://ftpmaster.internal vivid-proposed InRelease Get:2 http://ftpmaster.internal vivid Release.gpg [933 B] Get:3 http://ftpmaster.internal vivid-security Release.gpg [933 B] Get:4 http://ftpmaster.internal vivid-updates Release.gpg [933 B] Get:5 http://ftpmaster.internal vivid-proposed Release.gpg [933 B] Get:6 http://ftpmaster.internal vivid Release [112 kB] Get:7 http://archive-team.internal vivid/main amd64 Packages Ign http://archive-team.internal vivid/main Translation-en Get:8 http://ftpmaster.internal vivid-security Release [59.7 kB] Get:9 http://ftpmaster.internal vivid-updates Release [59.7 kB] Get:10 http://ftpmaster.internal vivid-proposed Release [59.7 kB] Get:11 http://ftpmaster.internal vivid/main amd64 Packages [1332 kB] Get:12 http://ftpmaster.internal vivid/universe amd64 Packages [6203 kB] Get:13 http://ftpmaster.internal vivid/main Translation-en [770 kB] Get:14 http://ftpmaster.internal vivid/universe Translation-en [4292 kB] Get:15 http://ftpmaster.internal vivid-security/main amd64 Packages [14 B] Get:16 http://ftpmaster.internal vivid-security/universe amd64 Packages [14 B] Get:17 http://ftpmaster.internal vivid-security/main Translation-en [14 B] Get:18 http://ftpmaster.internal vivid-security/universe Translation-en [14 B] Get:19 http://ftpmaster.internal vivid-updates/main amd64 Packages [14 B] Get:20 http://ftpmaster.internal vivid-updates/universe amd64 Packages [14 B] Get:21 http://ftpmaster.internal vivid-updates/main Translation-en [14 B] Get:22 http://ftpmaster.internal vivid-updates/universe Translation-en [14 B] Get:23 http://ftpmaster.internal vivid-proposed/main amd64 Packages [44.2 kB] Get:24 http://ftpmaster.internal vivid-proposed/universe amd64 Packages [310 kB] Get:25 http://ftpmaster.internal vivid-proposed/main Translation-en [44.4 kB] Get:26 http://ftpmaster.internal vivid-proposed/universe Translation-en [305 kB] Fetched 13.6 MB in 4s (3221 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: base-files binutils ca-certificates cpp-4.9 g++-4.9 gcc-4.9 gcc-4.9-base grep libacl1 libasan1 libatomic1 libcilkrts5 libdb5.3 libdrm2 libgcc-4.9-dev libgcc1 libgmp10 libgomp1 libgpg-error0 libgssapi-krb5-2 libitm1 libk5crypto3 libkrb5-3 libkrb5support0 liblsan0 libp11-kit0 libplymouth4 libquadmath0 libsasl2-2 libsasl2-modules-db libselinux1 libsqlite3-0 libstdc++-4.9-dev libstdc++6 libsystemd-journal0 libtasn1-6 libtsan0 libubsan0 libudev1 libusb-0.1-4 patch perl perl-base perl-modules plymouth tzdata udev 47 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 45.0 MB of archives. After this operation, 356 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu/ vivid/main base-files amd64 7.2ubuntu8 [63.5 kB] Get:2 http://ftpmaster.internal/ubuntu/ vivid/main grep amd64 2.20-4 [146 kB] Get:3 http://ftpmaster.internal/ubuntu/ vivid-proposed/main perl amd64 5.20.1-2 [2632 kB] Get:4 http://ftpmaster.internal/ubuntu/ vivid-proposed/main perl-base amd64 5.20.1-2 [1207 kB] Get:5 http://ftpmaster.internal/ubuntu/ vivid-proposed/main perl-modules all 5.20.1-2 [2531 kB] Get:6 http://ftpmaster.internal/ubuntu/ vivid/main libdb5.3 amd64 5.3.28-6 [671 kB] Get:7 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libubsan0 amd64 4.9.1-19ubuntu1 [83.7 kB] Get:8 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libtsan0 amd64 4.9.1-19ubuntu1 [216 kB] Get:9 http://ftpmaster.internal/ubuntu/ vivid-proposed/main gcc-4.9-base amd64 4.9.1-19ubuntu1 [15.6 kB] Get:10 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libstdc++6 amd64 4.9.1-19ubuntu1 [277 kB] Get:11 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libgomp1 amd64 4.9.1-19ubuntu1 [38.4 kB] Get:12 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libitm1 amd64 4.9.1-19ubuntu1 [30.1 kB] Get:13 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libatomic1 amd64 4.9.1-19ubuntu1 [9266 B] Get:14 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libasan1 amd64 4.9.1-19ubuntu1 [198 kB] Get:15 http://ftpmaster.internal/ubuntu/ vivid-proposed/main liblsan0 amd64 4.9.1-19ubuntu1 [94.0 kB] Get:16 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libcilkrts5 amd64 4.9.1-19ubuntu1 [40.5 kB] Get:17 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libquadmath0 amd64 4.9.1-19ubuntu1 [130 kB] Get:18 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libgcc-4.9-dev amd64 4.9.1-19ubuntu1 [2084 kB] Get:19 http://ftpmaster.internal/ubuntu/ vivid-proposed/main cpp-4.9 amd64 4.9.1-19ubuntu1 [5019 kB] Get:20 http://ftpmaster.internal/ubuntu/ vivid-proposed/main binutils amd64 2.24.90.20141023-1ubuntu1 [2198 kB] Get:21 http://ftpmaster.internal/ubuntu/ vivid-proposed/main gcc-4.9 amd64 4.9.1-19ubuntu1 [5638 kB] Get:22 http://ftpmaster.internal/ubuntu/ vivid-proposed/main g++-4.9 amd64 4.9.1-19ubuntu1 [17.5 MB] Get:23 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libstdc++-4.9-dev amd64 4.9.1-19ubuntu1 [1123 kB] Get:24 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libgcc1 amd64 1:4.9.1-19ubuntu1 [39.6 kB] Get:25 http://ftpmaster.internal/ubuntu/ vivid/main libgmp10 amd64 2:6.0.0+dfsg-6 [240 kB] Get:26 http://ftpmaster.internal/ubuntu/ vivid/main libusb-0.1-4 amd64 2:0.1.12-25 [16.6 kB] Get:27 http://ftpmaster.internal/ubuntu/ vivid/main libacl1 amd64 2.2.52-2 [16.3 kB] Get:28 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libgpg-error0 amd64 1.17-2 [32.2 kB] Get:29 http://ftpmaster.internal/ubuntu/ vivid/main libselinux1 amd64 2.3-2 [59.8 kB] Get:30 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libsystemd-journal0 amd64 215-5ubuntu1 [52.2 kB] Get:31 http://ftpmaster.internal/ubuntu/ vivid/main libp11-kit0 amd64 0.20.7-1 [77.1 kB] Get:32 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libsqlite3-0 amd64 3.8.7-1 [371 kB] Get:33 http://ftpmaster.internal/ubuntu/ vivid/main libtasn1-6 amd64 4.2-2 [42.1 kB] Get:34 http://ftpmaster.internal/ubuntu/ vivid/main libdrm2 amd64 2.4.58-2 [23.3 kB] Get:35 http://ftpmaster.internal/ubuntu/ vivid/main plymouth amd64 0.9.0-0ubuntu8 [103 kB] Get:36 http://ftpmaster.internal/ubuntu/ vivid-proposed/main udev amd64 215-5ubuntu1 [852 kB] Get:37 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libudev1 amd64 215-5ubuntu1 [33.9 kB] Get:38 http://ftpmaster.internal/ubuntu/ vivid/main libplymouth4 amd64 0.9.0-0ubuntu8 [85.9 kB] Get:39 http://ftpmaster.internal/ubuntu/ vivid/main libgssapi-krb5-2 amd64 1.12.1+dfsg-11 [119 kB] Get:40 http://ftpmaster.internal/ubuntu/ vivid/main libkrb5-3 amd64 1.12.1+dfsg-11 [270 kB] Get:41 http://ftpmaster.internal/ubuntu/ vivid/main libkrb5support0 amd64 1.12.1+dfsg-11 [30.7 kB] Get:42 http://ftpmaster.internal/ubuntu/ vivid/main libk5crypto3 amd64 1.12.1+dfsg-11 [82.4 kB] Get:43 http://ftpmaster.internal/ubuntu/ vivid/main libsasl2-modules-db amd64 2.1.26.dfsg1-12 [14.6 kB] Get:44 http://ftpmaster.internal/ubuntu/ vivid/main libsasl2-2 amd64 2.1.26.dfsg1-12 [49.5 kB] Get:45 http://ftpmaster.internal/ubuntu/ vivid/main tzdata all 2014i-1 [182 kB] Get:46 http://ftpmaster.internal/ubuntu/ vivid/main ca-certificates all 20141019 [192 kB] Get:47 http://ftpmaster.internal/ubuntu/ vivid/main patch amd64 2.7.1-6 [84.7 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 45.0 MB in 1s (36.0 MB/s) (Reading database ... 11482 files and directories currently installed.) Preparing to unpack .../base-files_7.2ubuntu8_amd64.deb ... Unpacking base-files (7.2ubuntu8) over (7.2ubuntu7) ... Setting up base-files (7.2ubuntu8) ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... Installing new version of config file /etc/os-release ... (Reading database ... 11482 files and directories currently installed.) Preparing to unpack .../archives/grep_2.20-4_amd64.deb ... Unpacking grep (2.20-4) over (2.20-3) ... Setting up grep (2.20-4) ... (Reading database ... 11482 files and directories currently installed.) Preparing to unpack .../perl_5.20.1-2_amd64.deb ... Unpacking perl (5.20.1-2) over (5.20.1-1) ... Preparing to unpack .../perl-base_5.20.1-2_amd64.deb ... Unpacking perl-base (5.20.1-2) over (5.20.1-1) ... Setting up perl-base (5.20.1-2) ... (Reading database ... 11482 files and directories currently installed.) 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Unpacking libplymouth4:amd64 (0.9.0-0ubuntu8) over (0.9.0-0ubuntu7) ... Preparing to unpack .../libgssapi-krb5-2_1.12.1+dfsg-11_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.12.1+dfsg-11) over (1.12.1+dfsg-10) ... Preparing to unpack .../libkrb5-3_1.12.1+dfsg-11_amd64.deb ... Unpacking libkrb5-3:amd64 (1.12.1+dfsg-11) over (1.12.1+dfsg-10) ... Preparing to unpack .../libkrb5support0_1.12.1+dfsg-11_amd64.deb ... Unpacking libkrb5support0:amd64 (1.12.1+dfsg-11) over (1.12.1+dfsg-10) ... Preparing to unpack .../libk5crypto3_1.12.1+dfsg-11_amd64.deb ... Unpacking libk5crypto3:amd64 (1.12.1+dfsg-11) over (1.12.1+dfsg-10) ... Preparing to unpack .../libsasl2-modules-db_2.1.26.dfsg1-12_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.26.dfsg1-12) over (2.1.26.dfsg1-11) ... Preparing to unpack .../libsasl2-2_2.1.26.dfsg1-12_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.26.dfsg1-12) over (2.1.26.dfsg1-11) ... Preparing to unpack .../tzdata_2014i-1_all.deb ... Unpacking tzdata (2014i-1) over (2014h-2) ... Setting up tzdata (2014i-1) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Oct 25 23:44:45 UTC 2014. Universal Time is now: Sat Oct 25 23:44:45 UTC 2014. Run 'dpkg-reconfigure tzdata' if you wish to change it. (Reading database ... 11492 files and directories currently installed.) Preparing to unpack .../ca-certificates_20141019_all.deb ... Unpacking ca-certificates (20141019) over (20140325) ... Preparing to unpack .../patch_2.7.1-6_amd64.deb ... Unpacking patch (2.7.1-6) over (2.7.1-5) ... Setting up libubsan0:amd64 (4.9.1-19ubuntu1) ... Setting up libtsan0:amd64 (4.9.1-19ubuntu1) ... Setting up libgomp1:amd64 (4.9.1-19ubuntu1) ... Setting up libitm1:amd64 (4.9.1-19ubuntu1) ... Setting up libatomic1:amd64 (4.9.1-19ubuntu1) ... Setting up libasan1:amd64 (4.9.1-19ubuntu1) ... Setting up liblsan0:amd64 (4.9.1-19ubuntu1) ... Setting up libcilkrts5:amd64 (4.9.1-19ubuntu1) ... Setting up libquadmath0:amd64 (4.9.1-19ubuntu1) ... Setting up libgcc-4.9-dev:amd64 (4.9.1-19ubuntu1) ... Setting up libgmp10:amd64 (2:6.0.0+dfsg-6) ... Setting up cpp-4.9 (4.9.1-19ubuntu1) ... Setting up binutils (2.24.90.20141023-1ubuntu1) ... Setting up gcc-4.9 (4.9.1-19ubuntu1) ... Setting up libstdc++-4.9-dev:amd64 (4.9.1-19ubuntu1) ... Setting up g++-4.9 (4.9.1-19ubuntu1) ... Setting up libp11-kit0:amd64 (0.20.7-1) ... Setting up libsqlite3-0:amd64 (3.8.7-1) ... Setting up libtasn1-6:amd64 (4.2-2) ... Setting up libdrm2:amd64 (2.4.58-2) ... Setting up libudev1:amd64 (215-5ubuntu1) ... Setting up libplymouth4:amd64 (0.9.0-0ubuntu8) ... Setting up udev (215-5ubuntu1) ... Installing new version of config file /etc/init.d/udev-finish ... A chroot environment has been detected, udev not started. update-initramfs: deferring update (trigger activated) Removing obsolete conffile /etc/udev/rules.d/README ... Setting up plymouth (0.9.0-0ubuntu8) ... update-initramfs: deferring update (trigger activated) Setting up libkrb5support0:amd64 (1.12.1+dfsg-11) ... Setting up libk5crypto3:amd64 (1.12.1+dfsg-11) ... Setting up libkrb5-3:amd64 (1.12.1+dfsg-11) ... Setting up libgssapi-krb5-2:amd64 (1.12.1+dfsg-11) ... Setting up libsasl2-modules-db:amd64 (2.1.26.dfsg1-12) ... Setting up libsasl2-2:amd64 (2.1.26.dfsg1-12) ... Setting up ca-certificates (20141019) ... Setting up patch (2.7.1-6) ... Setting up perl-modules (5.20.1-2) ... Setting up perl (5.20.1-2) ... Processing triggers for libc-bin (2.19-10ubuntu2) ... Processing triggers for initramfs-tools (0.103ubuntu8) ... Processing triggers for ca-certificates (20141019) ... Updating certificates in /etc/ssl/certs... 10 added, 5 removed; done. Running hooks in /etc/ca-certificates/update.d....done. RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-6502313', 'amd64', 'vivid-proposed', '--nolog', '--batch', '--archive=ubuntu', '--dist=vivid-proposed', '-A', '--purpose=PRIMARY', '--architecture=amd64', '--comp=universe', 'wise_2.4.1-17.dsc'] Initiating build PACKAGEBUILD-6502313 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 3.2.0-58-generic #88-Ubuntu SMP Tue Dec 3 17:37:58 UTC 2013 x86_64 Automatic build of wise_2.4.1-17 on kapok by sbuild/amd64 1.170.5 Build started at 20141025-2344 ****************************************************************************** wise_2.4.1-17.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 9), texlive-latex-base, texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev Checking for already installed source dependencies... debhelper: 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 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: bsdmainutils dh-apparmor docbook file fontconfig-config fonts-dejavu-core gettext gettext-base ghostscript groff-base gsfonts intltool-debian libasprintf0c2 libavahi-client3 libavahi-common-data libavahi-common3 libcroco3 libcups2 libcupsfilters1 libcupsimage2 libelfg0 libexpat1 libfontconfig1 libfreetype6 libglib2.0-0 libglib2.0-bin libglib2.0-data libgraphite2-3 libgs9 libgs9-common libharfbuzz-icu0 libharfbuzz0b libice6 libicu52 libijs-0.35 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libkpathsea6 liblcms2-2 libmagic1 libnetpbm10 libpaper-utils libpaper1 libpcre3-dev libpcrecpp0 libpipeline1 libpixman-1-0 libpoppler46 libpotrace0 libptexenc1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsm6 libsp1c2 libsynctex1 libtiff5 libunistring0 libx11-6 libx11-data libxau6 libxaw7 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxt6 libzzip-0-13 man-db mime-support netpbm ocaml-base-nox pkg-config po-debconf poppler-data python python-minimal python2.7 python2.7-minimal sgml-base sgml-data sp tex-common texlive-base texlive-binaries ucf x11-common xdg-utils xml-core zlib1g-dev Suggested packages: wamerican wordlist whois vacation dh-make apparmor-easyprof docbook-defguide docbook-dsssl docbook-xml psgml gettext-doc ghostscript-x hpijs groff hevea-doc texlive-latex-extra 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-nanum python-doc python-tk python2.7-doc binfmt-support sgml-base-doc perlsgml w3-recs opensp libxml2-utils doc-base gv postscript-viewer perl-tk xpdf-reader pdf-viewer latexdiff latexmk dvidvi fragmaster lacheck purifyeps xindy chktex dvipng gvfs-bin Recommended packages: curl wget lynx-cur libasprintf-dev libgettextpo-dev shared-mime-info xdg-user-dirs libmail-sendmail-perl lmodern ruby wish texlive-latex-recommended libfile-homedir-perl libyaml-tiny-perl texlive-latex-base-doc libfile-mimeinfo-perl x11-utils x11-xserver-utils The following NEW packages will be installed: bsdmainutils debhelper dh-apparmor docbook docbook-to-man file fontconfig-config fonts-dejavu-core gettext gettext-base ghostscript groff-base gsfonts hevea intltool-debian libasprintf0c2 libavahi-client3 libavahi-common-data libavahi-common3 libcroco3 libcups2 libcupsfilters1 libcupsimage2 libelfg0 libexpat1 libfontconfig1 libfreetype6 libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev libgraphite2-3 libgs9 libgs9-common libharfbuzz-icu0 libharfbuzz0b libice6 libicu52 libijs-0.35 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libkpathsea6 liblcms2-2 libmagic1 libnetpbm10 libpaper-utils libpaper1 libpcre3-dev libpcrecpp0 libpipeline1 libpixman-1-0 libpoppler46 libpotrace0 libptexenc1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libsm6 libsp1c2 libsynctex1 libtiff5 libunistring0 libx11-6 libx11-data libxau6 libxaw7 libxcb1 libxdmcp6 libxext6 libxi6 libxml2 libxmu6 libxpm4 libxt6 libzzip-0-13 man-db mime-support netpbm ocaml-base-nox pkg-config po-debconf poppler-data python python-minimal python2.7 python2.7-minimal sgml-base sgml-data sp tex-common texlive-base texlive-binaries texlive-extra-utils texlive-latex-base ucf x11-common xdg-utils xml-core zlib1g-dev 0 upgraded, 101 newly installed, 0 to remove and 0 not upgraded. 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Get:1 http://ftpmaster.internal/ubuntu/ vivid/main libexpat1 amd64 2.1.0-6ubuntu1 [70.6 kB] Get:2 http://ftpmaster.internal/ubuntu/ vivid/main libmagic1 amd64 1:5.19-1ubuntu1.1 [201 kB] Get:3 http://ftpmaster.internal/ubuntu/ vivid/main libasprintf0c2 amd64 0.19.2-2ubuntu1 [6296 B] Get:4 http://ftpmaster.internal/ubuntu/ vivid/main libglib2.0-0 amd64 2.42.0-2 [1088 kB] Get:5 http://ftpmaster.internal/ubuntu/ vivid/main libpipeline1 amd64 1.3.1-1 [24.4 kB] Get:6 http://ftpmaster.internal/ubuntu/ vivid/main libxau6 amd64 1:1.0.8-1 [8376 B] Get:7 http://ftpmaster.internal/ubuntu/ vivid/main libxdmcp6 amd64 1:1.1.1-1build1 [11.0 kB] Get:8 http://ftpmaster.internal/ubuntu/ vivid/main libxcb1 amd64 1.10-2ubuntu1 [38.0 kB] Get:9 http://ftpmaster.internal/ubuntu/ vivid/main libx11-data all 2:1.6.2-2ubuntu2 [112 kB] Get:10 http://ftpmaster.internal/ubuntu/ vivid/main libx11-6 amd64 2:1.6.2-2ubuntu2 [571 kB] Get:11 http://ftpmaster.internal/ubuntu/ vivid/main libxext6 amd64 2:1.3.3-1 [29.4 kB] Get:12 http://ftpmaster.internal/ubuntu/ vivid/main libxml2 amd64 2.9.1+dfsg1-4ubuntu1 [580 kB] Get:13 http://ftpmaster.internal/ubuntu/ vivid/main groff-base amd64 1.22.2-8 [1165 kB] Get:14 http://ftpmaster.internal/ubuntu/ vivid/main bsdmainutils amd64 9.0.5ubuntu1 [203 kB] Get:15 http://ftpmaster.internal/ubuntu/ vivid/main man-db amd64 2.7.0.2-2 [863 kB] Get:16 http://ftpmaster.internal/ubuntu/ vivid/main sgml-base all 1.26+nmu4ubuntu1 [12.5 kB] Get:17 http://ftpmaster.internal/ubuntu/ vivid/main libavahi-common-data amd64 0.6.31-4ubuntu3 [21.2 kB] Get:18 http://ftpmaster.internal/ubuntu/ vivid/main libavahi-common3 amd64 0.6.31-4ubuntu3 [22.1 kB] Get:19 http://ftpmaster.internal/ubuntu/ vivid/main libavahi-client3 amd64 0.6.31-4ubuntu3 [25.7 kB] Get:20 http://ftpmaster.internal/ubuntu/ vivid/main libcroco3 amd64 0.6.8-3 [83.2 kB] Get:21 http://ftpmaster.internal/ubuntu/ vivid/main libcups2 amd64 1.7.5-3ubuntu2 [183 kB] Get:22 http://ftpmaster.internal/ubuntu/ vivid/main libjpeg-turbo8 amd64 1.3.0-0ubuntu2 [104 kB] Get:23 http://ftpmaster.internal/ubuntu/ vivid/main libjpeg8 amd64 8c-2ubuntu8 [2194 B] Get:24 http://ftpmaster.internal/ubuntu/ vivid/main libjbig0 amd64 2.1-3ubuntu1 [26.8 kB] Get:25 http://ftpmaster.internal/ubuntu/ vivid/main libtiff5 amd64 4.0.3-10build1 [145 kB] Get:26 http://ftpmaster.internal/ubuntu/ vivid/main libcupsfilters1 amd64 1.0.61-0ubuntu2 [80.3 kB] Get:27 http://ftpmaster.internal/ubuntu/ vivid/main libcupsimage2 amd64 1.7.5-3ubuntu2 [15.2 kB] Get:28 http://ftpmaster.internal/ubuntu/ vivid/main libelfg0 amd64 0.8.13-5 [37.6 kB] Get:29 http://ftpmaster.internal/ubuntu/ vivid/main fonts-dejavu-core all 2.34-1ubuntu1 [1024 kB] Get:30 http://ftpmaster.internal/ubuntu/ vivid/main ucf all 3.0030 [55.5 kB] Get:31 http://ftpmaster.internal/ubuntu/ vivid/main fontconfig-config all 2.11.1-0ubuntu3 [48.7 kB] Get:32 http://ftpmaster.internal/ubuntu/ vivid/main libfreetype6 amd64 2.5.2-2ubuntu1 [315 kB] Get:33 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[15.2 kB] Get:44 http://ftpmaster.internal/ubuntu/ vivid/main libpixman-1-0 amd64 0.32.4-1ubuntu1 [228 kB] Get:45 http://ftpmaster.internal/ubuntu/ vivid/main libpoppler46 amd64 0.26.5-0ubuntu1 [752 kB] Get:46 http://ftpmaster.internal/ubuntu/ vivid/main libsm6 amd64 2:1.2.2-1 [15.8 kB] Get:47 http://ftpmaster.internal/ubuntu/ vivid/main libunistring0 amd64 0.9.3-5ubuntu3 [271 kB] Get:48 http://ftpmaster.internal/ubuntu/ vivid/main libxt6 amd64 1:1.1.4-1 [185 kB] Get:49 http://ftpmaster.internal/ubuntu/ vivid/main libxmu6 amd64 2:1.1.2-1 [45.3 kB] Get:50 http://ftpmaster.internal/ubuntu/ vivid/main libxpm4 amd64 1:3.5.11-1 [33.1 kB] Get:51 http://ftpmaster.internal/ubuntu/ vivid/main libxaw7 amd64 2:1.0.12-2 [168 kB] Get:52 http://ftpmaster.internal/ubuntu/ vivid/main libxi6 amd64 2:1.7.4-1 [28.5 kB] Get:53 http://ftpmaster.internal/ubuntu/ vivid/main libzzip-0-13 amd64 0.13.62-3 [26.1 kB] Get:54 http://ftpmaster.internal/ubuntu/ vivid/main poppler-data all 0.4.7-1 [1476 kB] Get:55 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texlive-binaries amd64 2014.20140926.35254-2 [8356 kB] Get:87 http://ftpmaster.internal/ubuntu/ vivid/main texlive-base all 2014.20140717-01ubuntu1 [17.7 MB] Get:88 http://ftpmaster.internal/ubuntu/ vivid/main ocaml-base-nox amd64 4.01.0-4ubuntu1 [447 kB] Get:89 http://ftpmaster.internal/ubuntu/ vivid/main hevea all 2.18-1 [309 kB] Get:90 http://ftpmaster.internal/ubuntu/ vivid/main libglib2.0-bin amd64 2.42.0-2 [39.1 kB] Get:91 http://ftpmaster.internal/ubuntu/ vivid/main libpython2.7-stdlib amd64 2.7.8-10ubuntu1 [1839 kB] Get:92 http://ftpmaster.internal/ubuntu/ vivid/main python2.7 amd64 2.7.8-10ubuntu1 [204 kB] Get:93 http://ftpmaster.internal/ubuntu/ vivid-proposed/main python-minimal amd64 2.7.8-2 [28.4 kB] Get:94 http://ftpmaster.internal/ubuntu/ vivid-proposed/main libpython-stdlib amd64 2.7.8-2 [7852 B] Get:95 http://ftpmaster.internal/ubuntu/ vivid-proposed/main python amd64 2.7.8-2 [137 kB] Get:96 http://ftpmaster.internal/ubuntu/ vivid/main libpcre3-dev amd64 1:8.35-3ubuntu1 [333 kB] Get:97 http://ftpmaster.internal/ubuntu/ vivid/main pkg-config amd64 0.28-1ubuntu1 [40.0 kB] Get:98 http://ftpmaster.internal/ubuntu/ vivid/main zlib1g-dev amd64 1:1.2.8.dfsg-1ubuntu1 [183 kB] Get:99 http://ftpmaster.internal/ubuntu/ vivid/main libglib2.0-dev amd64 2.42.0-2 [1348 kB] Get:100 http://ftpmaster.internal/ubuntu/ vivid/main texlive-latex-base all 2014.20140717-01ubuntu1 [840 kB] Get:101 http://ftpmaster.internal/ubuntu/ vivid-proposed/main texlive-extra-utils all 2014.20141024-1 [10.4 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 75.0 MB in 2s (26.5 MB/s) Selecting previously unselected package libexpat1:amd64. (Reading database ... 11497 files and directories currently installed.) Preparing to unpack .../libexpat1_2.1.0-6ubuntu1_amd64.deb ... Unpacking libexpat1:amd64 (2.1.0-6ubuntu1) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../libmagic1_1%3a5.19-1ubuntu1.1_amd64.deb ... Unpacking libmagic1:amd64 (1:5.19-1ubuntu1.1) ... Selecting previously unselected package libasprintf0c2:amd64. Preparing to unpack .../libasprintf0c2_0.19.2-2ubuntu1_amd64.deb ... Unpacking libasprintf0c2:amd64 (0.19.2-2ubuntu1) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../libglib2.0-0_2.42.0-2_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.42.0-2) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../libpipeline1_1.3.1-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.3.1-1) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../libxau6_1%3a1.0.8-1_amd64.deb ... 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Unpacking texlive-latex-base (2014.20140717-01ubuntu1) ... Selecting previously unselected package texlive-extra-utils. Preparing to unpack .../texlive-extra-utils_2014.20141024-1_all.deb ... Unpacking texlive-extra-utils (2014.20141024-1) ... Setting up libexpat1:amd64 (2.1.0-6ubuntu1) ... Setting up libmagic1:amd64 (1:5.19-1ubuntu1.1) ... Setting up libasprintf0c2:amd64 (0.19.2-2ubuntu1) ... Setting up libglib2.0-0:amd64 (2.42.0-2) ... No schema files found: doing nothing. Setting up libpipeline1:amd64 (1.3.1-1) ... Setting up libxau6:amd64 (1:1.0.8-1) ... Setting up libxdmcp6:amd64 (1:1.1.1-1build1) ... Setting up libxcb1:amd64 (1.10-2ubuntu1) ... Setting up libx11-data (2:1.6.2-2ubuntu2) ... Setting up libx11-6:amd64 (2:1.6.2-2ubuntu2) ... Setting up libxext6:amd64 (2:1.3.3-1) ... Setting up libxml2:amd64 (2.9.1+dfsg1-4ubuntu1) ... Setting up groff-base (1.22.2-8) ... 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 (2.7.0.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up sgml-base (1.26+nmu4ubuntu1) ... Setting up libavahi-common-data:amd64 (0.6.31-4ubuntu3) ... Setting up libavahi-common3:amd64 (0.6.31-4ubuntu3) ... Setting up libavahi-client3:amd64 (0.6.31-4ubuntu3) ... Setting up libcroco3:amd64 (0.6.8-3) ... Setting up libcups2:amd64 (1.7.5-3ubuntu2) ... Setting up libjpeg-turbo8:amd64 (1.3.0-0ubuntu2) ... Setting up libjpeg8:amd64 (8c-2ubuntu8) ... Setting up libjbig0:amd64 (2.1-3ubuntu1) ... Setting up libtiff5:amd64 (4.0.3-10build1) ... Setting up libcupsfilters1:amd64 (1.0.61-0ubuntu2) ... Setting up libcupsimage2:amd64 (1.7.5-3ubuntu2) ... Setting up libelfg0:amd64 (0.8.13-5) ... Setting up fonts-dejavu-core (2.34-1ubuntu1) ... Setting up ucf (3.0030) ... Setting up fontconfig-config (2.11.1-0ubuntu3) ... Setting up libfreetype6:amd64 (2.5.2-2ubuntu1) ... Setting up libfontconfig1:amd64 (2.11.1-0ubuntu3) ... Setting up libgraphite2-3:amd64 (1.2.4-3ubuntu1) ... Setting up libharfbuzz0b:amd64 (0.9.35-1) ... Setting up libicu52:amd64 (52.1-6) ... Setting up libharfbuzz-icu0:amd64 (0.9.35-1) ... Setting up x11-common (1:7.7+7ubuntu2) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults invoke-rc.d: policy-rc.d denied execution of start. Setting up libice6:amd64 (2:1.0.9-1) ... Setting up libijs-0.35:amd64 (0.35-10) ... Setting up liblcms2-2:amd64 (2.6-3ubuntu1) ... Setting up libpaper1:amd64 (1.1.24+nmu2ubuntu3) ... Creating config file /etc/papersize with new version Setting up libpcrecpp0:amd64 (1:8.35-3ubuntu1) ... Setting up libpixman-1-0:amd64 (0.32.4-1ubuntu1) ... Setting up libpoppler46:amd64 (0.26.5-0ubuntu1) ... Setting up libsm6:amd64 (2:1.2.2-1) ... Setting up libunistring0:amd64 (0.9.3-5ubuntu3) ... Setting up libxt6:amd64 (1:1.1.4-1) ... Setting up libxmu6:amd64 (2:1.1.2-1) ... Setting up libxpm4:amd64 (1:3.5.11-1) ... Setting up libxaw7:amd64 (2:1.0.12-2) ... Setting up libxi6:amd64 (2:1.7.4-1) ... Setting up libzzip-0-13:amd64 (0.13.62-3) ... Setting up poppler-data (0.4.7-1) ... Setting up libpython2.7-minimal:amd64 (2.7.8-10ubuntu1) ... Setting up python2.7-minimal (2.7.8-10ubuntu1) ... Linking and byte-compiling packages for runtime python2.7... Setting up file (1:5.19-1ubuntu1.1) ... Setting up mime-support (3.55ubuntu1) ... Setting up gettext-base (0.19.2-2ubuntu1) ... Setting up libglib2.0-data (2.42.0-2) ... Setting up xml-core (0.13+nmu2) ... Setting up gettext (0.19.2-2ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu3) ... Setting up dh-apparmor (2.8.98-0ubuntu2) ... Setting up debhelper (9.20141003ubuntu1) ... Setting up libsp1c2 (1.3.4-1.2.1-47.3ubuntu1) ... Setting up sp (1.3.4-1.2.1-47.3ubuntu1) ... Setting up libjbig2dec0 (0.11+20120125-1ubuntu1) ... Setting up libgs9-common (9.14~dfsg-0ubuntu3) ... update-alternatives: using /usr/share/ghostscript/9.14 to provide /usr/share/ghostscript/current (ghostscript-current) in auto mode Setting up libgs9 (9.14~dfsg-0ubuntu3) ... Setting up gsfonts (1:8.11+urwcyr1.0.7~pre44-4.2ubuntu1) ... Setting up ghostscript (9.14~dfsg-0ubuntu3) ... Setting up libnetpbm10 (2:10.0-15.1) ... Setting up netpbm (2:10.0-15.1) ... Setting up libpaper-utils (1.1.24+nmu2ubuntu3) ... Setting up xdg-utils (1.1.0~rc1-2ubuntu8) ... Setting up tex-common (5.03) ... Setting up libkpathsea6 (2014.20140926.35254-2) ... Setting up libptexenc1 (2014.20140926.35254-2) ... Setting up libpotrace0 (1.11-2) ... Setting up libsynctex1 (2014.20140926.35254-2) ... Setting up texlive-binaries (2014.20140926.35254-2) ... 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 texlive-base (2014.20140717-01ubuntu1) ... /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 (4.01.0-4ubuntu1) ... Setting up libglib2.0-bin (2.42.0-2) ... Setting up libpython2.7-stdlib:amd64 (2.7.8-10ubuntu1) ... Setting up python2.7 (2.7.8-10ubuntu1) ... Setting up python-minimal (2.7.8-2) ... Setting up libpython-stdlib:amd64 (2.7.8-2) ... Setting up python (2.7.8-2) ... Setting up libpcre3-dev:amd64 (1:8.35-3ubuntu1) ... Setting up pkg-config (0.28-1ubuntu1) ... Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-1ubuntu1) ... Setting up libglib2.0-dev (2.42.0-2) ... Processing triggers for tex-common (5.03) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Setting up hevea (2.18-1) ... Setting up texlive-latex-base (2014.20140717-01ubuntu1) ... 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 (5.03) ... 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 (2014.20141024-1) ... Processing triggers for sgml-base (1.26+nmu4ubuntu1) ... Setting up sgml-data (2.0.10) ... Processing triggers for sgml-base (1.26+nmu4ubuntu1) ... Setting up docbook (4.5-5.1ubuntu1) ... Processing triggers for sgml-base (1.26+nmu4ubuntu1) ... Setting up docbook-to-man (1:2.0.0-32) ... Processing triggers for libc-bin (2.19-10ubuntu2) ... Processing triggers for tex-common (5.03) ... Running mktexlsr. This may take some time... done. Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.19-10ubuntu2 make_4.0-8 dpkg-dev_1.17.13ubuntu1 gcc-4.9_4.9.1-19ubuntu1 g++-4.9_4.9.1-19ubuntu1 binutils_2.24.90.20141023-1ubuntu1 libstdc++-4.9-dev_4.9.1-19ubuntu1 libstdc++6_4.9.1-19ubuntu1 ------------------------------------------------------------------------------ dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::Quilt gpgv: Signature made Tue Sep 23 12:51:55 2014 UTC using RSA key ID 2295D502 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./wise_2.4.1-17.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_2.4.1-17.debian.tar.xz 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-source: info: applying 09_dnal-add-return-statement.patch dpkg-source: info: applying 10_fix_path_to_data_files.patch dpkg-buildpackage: source package wise dpkg-buildpackage: source version 2.4.1-17 dpkg-buildpackage: source distribution unstable dpkg-source --before-build wise-2.4.1 dpkg-buildpackage: host architecture amd64 /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 . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS \) -prune -o -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-strong -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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include wiseconfig.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include wisestring.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include wiseerror.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include wisememman.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include wiserandom.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include wisetime.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include wiseoverlay.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include wisestreaminterface.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include commandline.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-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-strong -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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c alphabet.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c core_algorithms.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c debug.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c emit.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c emulation.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c histogram.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c hmmio.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c mathsupport.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c masks.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c misc.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c modelmakers.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c plan7.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c plan9.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c prior.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c tophits.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c trace.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c aligneval.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c alignio.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c cluster.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c dayhoff.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c file.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c getopt.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c gnuregex.c gnuregex.c: In function 're_match_2': gnuregex.c:3752:31: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] if ((int) old_regend[r] >= (int) regstart[r]) ^ gnuregex.c:3752:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] if ((int) old_regend[r] >= (int) regstart[r]) ^ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2394:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^ gnuregex.c:3758:19: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (p1 + mcnt, d, -2); ^ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2397:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' PUSH_FAILURE_ITEM (highest_active_reg); \ ^ gnuregex.c:3758:19: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (p1 + mcnt, d, -2); ^ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2394:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^ gnuregex.c:3905:11: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (p + mcnt, NULL, -2); ^ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2397:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' PUSH_FAILURE_ITEM (highest_active_reg); \ ^ gnuregex.c:3905:11: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (p + mcnt, NULL, -2); ^ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2394:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^ gnuregex.c:3958:11: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (p + mcnt, d, -2); ^ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2397:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' PUSH_FAILURE_ITEM (highest_active_reg); \ ^ gnuregex.c:3958:11: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (p + mcnt, d, -2); ^ gnuregex.c:2482:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] high_reg = (unsigned) POP_FAILURE_ITEM (); \ ^ gnuregex.c:4064:13: note: in expansion of macro 'POP_FAILURE_POINT' POP_FAILURE_POINT (sdummy, pdummy, ^ gnuregex.c:2485:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] low_reg = (unsigned) POP_FAILURE_ITEM (); \ ^ gnuregex.c:4064:13: note: in expansion of macro 'POP_FAILURE_POINT' POP_FAILURE_POINT (sdummy, pdummy, ^ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2394:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^ gnuregex.c:4097:11: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (0, 0, -2); ^ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2397:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' PUSH_FAILURE_ITEM (highest_active_reg); \ ^ gnuregex.c:4097:11: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (0, 0, -2); ^ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2394:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^ gnuregex.c:4110:11: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (0, 0, -2); ^ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2397:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' PUSH_FAILURE_ITEM (highest_active_reg); \ ^ gnuregex.c:4110:11: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (0, 0, -2); ^ gnuregex.c:2482:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] high_reg = (unsigned) POP_FAILURE_ITEM (); \ ^ gnuregex.c:4278:11: note: in expansion of macro 'POP_FAILURE_POINT' POP_FAILURE_POINT (d, p, ^ gnuregex.c:2485:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] low_reg = (unsigned) POP_FAILURE_ITEM (); \ ^ gnuregex.c:4278:11: note: in expansion of macro 'POP_FAILURE_POINT' POP_FAILURE_POINT (d, p, ^ cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c interleaved.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c iupac.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c msf.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c revcomp.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c selex.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c sqerror.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c sqio.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c sre_ctype.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c sre_math.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c sre_string.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c stack.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c translate.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -c types.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-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-strong -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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ packaln.c packaln.dy: In function 'Wise2_read_simple_PackAln': packaln.dy:88:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(buffer,MAXLINE,ifp); ^ cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ dnamatrix.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ probability.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ alnrange.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ alnconvert.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ basematrix.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ shattermatrix.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ matrixdebug.c matrixdebug.dy: In function 'Wise2_user_DebugMatrix': matrixdebug.dy:208:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(buffer,MAXLINE,in); ^ cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ dpenvelope.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ dbsearchimpl.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ dprunimpl.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ complexsequence.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ complexevalset.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ complexconsensi.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ sequence.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ sequencestream.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ seqalign.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ hitlist.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ hsp.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ hspstream.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ codon.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ compmat.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ codonmatrix.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ codonmapper.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ sequencedb.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ hscore.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ seqlookup.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ arrayseqlookup.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ genericindexresult.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ linkedlist_lookpos.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ singlenumberspace.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ histogram.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ searchstatinterface.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ searchstatlookup.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ proteindb.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ protein.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ pairbase.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ pairbaseseq.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ genomicdb.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ randommodel.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ randomdb.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ genomic.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ cdna.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ cdnadb.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ dna.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ embl.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ genomicregion.c genomicregion.dy: In function 'Wise2_read_EMBL_FT_into_GenomicRegion': genomicregion.dy:756:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(buffer,maxlen,ifp); ^ cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ gene.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ transcript.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ translation.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ btcanvas.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ asciibtcanvas.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-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-strong -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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ subseqhash.c subseqhash.dy: In function 'Wise2_is_populated_subseqhash_ghash': subseqhash.dy:111:29: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] if( g_hash_table_lookup(h,(gconstpointer)seq_number) == NULL ) { ^ subseqhash.dy: In function 'Wise2_lookup_subseqhash_ghash': subseqhash.dy:128:85: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] return new_linkedl_SeqLookupResultInterface((SeqLookupPos *)g_hash_table_lookup(h,(gconstpointer)seq_number)); ^ subseqhash.dy: In function 'Wise2_add_seq_subseqhash_ghash': subseqhash.dy:160:54: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] if((ret = (SeqLookupPos *) g_hash_table_lookup(h,(gconstpointer)seq_number)) == NULL ) { ^ subseqhash.dy:161:29: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] g_hash_table_insert(h,(gpointer)seq_number,p); ^ subseqhash.dy: In function 'Wise2_add_direct_number_subseqhash_ghash': subseqhash.dy:188:52: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] if((ret = (SeqLookupPos *) g_hash_table_lookup(h,(gconstpointer)seq_number)) == NULL ) { ^ subseqhash.dy:189:27: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] g_hash_table_insert(h,(gpointer)seq_number,p); ^ cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ intallocator.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ proteinstreamedindex.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ shadowseq.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-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 'long unsigned int' [-Wformat=] fprintf(ofp,"Head memory %d [%.2f Mbytes]\n",total_head,(total_head*sizeof(ShadowArraySeqHead))/100000); ^ cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ hsphandler.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ hspscaninterface.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-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 '__time_t' [-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 '__time_t' [-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 '__time_t' [-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 '__time_t' [-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 '__time_t' [-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 '__time_t' [-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 '__time_t' [-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 '__time_t' [-Wformat=] cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ hsplookupscan.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ hspthreadeddb.c hspthreadeddb.dy: In function 'Wise2_threadeddb_scan_worker': hspthreadeddb.dy:154:77: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] fprintf(stderr,"For segment %d, finished query with %d (%d) linear\n",seg,(int)seg->lm,seg->lm->len); ^ 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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ hspscanruntime.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ hsptwohitscan.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ proteinindexcons.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ dnaindexcons.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-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-strong -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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-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' free(freq0); ^ mott_api.c: In function 'SW_PValueMott': mott_api.c:104:7: warning: incompatible implicit declaration of built-in function 'free' free(freqA); ^ mott_api.c: In function 'KarlinAltschulStatistics2': mott_api.c:144:5: warning: incompatible implicit declaration of built-in function 'free' free(h+hmin); ^ mott_api.c:155:5: warning: incompatible implicit declaration of built-in function 'free' free(h+hmin); ^ mott_api.c: In function 'GetHistogram': mott_api.c:179:16: warning: incompatible implicit declaration of built-in function 'calloc' 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' double *freq = (double*)calloc(256, sizeof(double)); ^ cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -D_FORTIFY_SOURCE=2 -c -o gaplib.o gaplib.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-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-strong -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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ functionserver.c functionserver.dy: In function 'Wise2_main_loop_forking_FunctionServer': functionserver.dy:129:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(new_socket,buf,9); ^ functionserver.dy:141:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(new_socket,buf,6); ^ functionserver.dy:183:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(new_socket,buf,5); ^ cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ functionclient.c functionclient.dy: In function 'Wise2_new_FunctionProxyCoordinator': functionclient.dy:193:24: warning: passing argument 2 of 'connect' from incompatible pointer type connect(out->socket, &server, sizeof(server)); ^ In file included from functionclient.c:7:0: /usr/include/x86_64-linux-gnu/sys/socket.h:137:12: 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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ anonobj.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ transferinterface.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-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-strong -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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_index_interface.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_direct.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_count.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_glib_index.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models singleseqspace.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models dnamapping.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models largeseqreader.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_untangler.c kmer_assembly_untangler.dy: In function 'Wise2_show_KmerAssemblyPath': kmer_assembly_untangler.dy:52:65: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] fprintf(ofp,"%3d memory %d, from [%s] to [%s], base %c\n",i,(int)kap->stack[i],back,forw,kap->stack[i]->base); ^ 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:568:75: warning: passing argument 4 of 'Wise2_lift_backward_tangled_tail' from incompatible pointer type 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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_contig.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-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 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-strong -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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex wise_proteinindex_server.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-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-strong -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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dnal.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dnaalign.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ psw.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ proteinsw.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ sw_wrap.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ abc.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dbac.c dbac.c: In function 'make_SeqAlign_from_align': dbac.c:413:3: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' [-Wformat=] fprintf(stderr,"Got %d with %d vs %d\n",i,strlen(seq),one->len); ^ cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dba.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ slimdba.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ bigdba.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include estwise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparser21.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparameter.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genestats.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisehsp.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneutil.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneoutput.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ threestatemodel.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genefrequency.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ splicesitemodeler.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise4.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise6.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genestretch6.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise21.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneloop21.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneloop6.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genephase6.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ gwlite.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ gwlitemodel.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ gwrap.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ matchsum.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estwrap.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisemodel.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ phasemodel.c phasemodel.dy: In function 'Wise2_read_fasta_PhasedProtein': phasemodel.dy:241:3: 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:241:3: /usr/include/x86_64-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 return __fgets_chk_warn (__s, __bos (__s), __n, __stream); ^ cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ cdparser.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estwise3.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estslim3.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estloop3.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estfrag3.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estslimloop.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ gwquickdb.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ threestatedb.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pfamhmmer1db.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pwmdna.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../HMMer2/ -DHMMER_INTERNAL -I../base/ -I../dynlibsrc/ wise2xhmmer2.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisemodeldb.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ seqhit.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ standardout.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparser4.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genomewise.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genomewise9.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genome_evidence.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-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 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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ sywise.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ sywise20.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pseudowise.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-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-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` promoterwise.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ localdba.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` localcishit.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ localcispara.c cc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/x86_64-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 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 3.14159265-2.6-1.40.15 (TeX Live 2015/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./api.tex LaTeX2e <2014/05/01> Babel <3.9k> 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, 304025 bytes). Transcript written on api.log. cd docs && pdflatex api.tex This is pdfTeX, Version 3.14159265-2.6-1.40.15 (TeX Live 2015/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./api.tex LaTeX2e <2014/05/01> Babel <3.9k> 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, 318612 bytes). Transcript written on api.log. cd docs && pdflatex dynamite.tex This is pdfTeX, Version 3.14159265-2.6-1.40.15 (TeX Live 2015/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./dynamite.tex LaTeX2e <2014/05/01> Babel <3.9k> 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, 214227 bytes). Transcript written on dynamite.log. cd docs && pdflatex dynamite.tex This is pdfTeX, Version 3.14159265-2.6-1.40.15 (TeX Live 2015/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./dynamite.tex LaTeX2e <2014/05/01> Babel <3.9k> 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, 217768 bytes). Transcript written on dynamite.log. cd docs && pdflatex wise2.tex This is pdfTeX, Version 3.14159265-2.6-1.40.15 (TeX Live 2015/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./wise2.tex LaTeX2e <2014/05/01> Babel <3.9k> 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, 205915 bytes). Transcript written on wise2.log. cd docs && pdflatex wise2.tex This is pdfTeX, Version 3.14159265-2.6-1.40.15 (TeX Live 2015/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./wise2.tex LaTeX2e <2014/05/01> Babel <3.9k> 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, 208429 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 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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' debian/rules override_dh_auto_test make[1]: Entering directory '/build/buildd/wise-2.4.1' echo "Since a patch was used to adapt the binaries to the Debian locations of data files the test suite will not run in the build directory any more." Since a patch was used to adapt the binaries to the Debian locations of data files the test suite will not run in the build directory any more. echo "A autopkgtest was added as compensation." A autopkgtest was added as compensation. # make -C src test make[1]: Leaving directory '/build/buildd/wise-2.4.1' /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 cp -a debian/tests/run-unit-test 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 -print0 | xargs -0 -I {} 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 -print0 | xargs -0 -I {} 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 -print0 | xargs -0 -I {} 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.wise debian/wise-doc/usr/share/doc-base/wise 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.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 debian/rules override_dh_installexamples-indep make[1]: Entering directory '/build/buildd/wise-2.4.1' dh_installexamples install -d debian/wise-data/usr/share/doc/wise-data/examples cp -a src/test/basic_cdna.out debian/wise-data/usr/share/doc/wise-data/examples cp -a src/test/basic_dna.out debian/wise-data/usr/share/doc/wise-data/examples cp -a src/test/basic_genomic.out debian/wise-data/usr/share/doc/wise-data/examples cp -a src/test/dna.db debian/wise-data/usr/share/doc/wise-data/examples cp -a src/test/estwise-db.out debian/wise-data/usr/share/doc/wise-data/examples cp -a src/test/genewise-db-lite.out debian/wise-data/usr/share/doc/wise-data/examples cp -a src/test/genewise-db.out debian/wise-data/usr/share/doc/wise-data/examples cp -a src/test/genewisedb-pfam.out debian/wise-data/usr/share/doc/wise-data/examples cp -a src/test/go.evi debian/wise-data/usr/share/doc/wise-data/examples cp -a src/test/go.out debian/wise-data/usr/share/doc/wise-data/examples cp -a src/test/HMM.ascii debian/wise-data/usr/share/doc/wise-data/examples cp -a src/test/HMM.binary debian/wise-data/usr/share/doc/wise-data/examples cp -a src/test/hmm_cdna.out debian/wise-data/usr/share/doc/wise-data/examples cp -a src/test/hmm_genomic.out debian/wise-data/usr/share/doc/wise-data/examples cp -a src/test/human.genomic debian/wise-data/usr/share/doc/wise-data/examples cp -a src/test/pep.fa debian/wise-data/usr/share/doc/wise-data/examples cp -a src/test/promoterwise.out debian/wise-data/usr/share/doc/wise-data/examples cp -a src/test/pswdb.out debian/wise-data/usr/share/doc/wise-data/examples cp -a src/test/pw.human debian/wise-data/usr/share/doc/wise-data/examples cp -a src/test/pw.mouse debian/wise-data/usr/share/doc/wise-data/examples cp -a src/test/road.pep debian/wise-data/usr/share/doc/wise-data/examples cp -a src/test/rrm.HMM debian/wise-data/usr/share/doc/wise-data/examples cp -a src/test/scanwisep.out debian/wise-data/usr/share/doc/wise-data/examples cp -a src/test/short.dna debian/wise-data/usr/share/doc/wise-data/examples cp -a src/test/short.pep debian/wise-data/usr/share/doc/wise-data/examples cp -a src/test/short.test debian/wise-data/usr/share/doc/wise-data/examples cp -a src/test/testman.pl debian/wise-data/usr/share/doc/wise-data/examples cp -a src/test/wrong.hmm debian/wise-data/usr/share/doc/wise-data/examples cp -a src/test/wrong.out debian/wise-data/usr/share/doc/wise-data/examples cp -a src/test/wrong_est.out debian/wise-data/usr/share/doc/wise-data/examples sed -i -e 's?"../bin/$do"?"$do"?' -e 's?#!/usr/local/bin/perl?/usr/bin/perl?' debian/wise-data/usr/share/doc/wise-data/examples/testman.pl make[1]: Leaving directory '/build/buildd/wise-2.4.1' 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 ./genomewise\.1 > genomewise\.1\.new chmod 644 genomewise.1.new mv -f genomewise.1.new genomewise.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 ./estwisedb\.1 > estwisedb\.1\.new chmod 644 estwisedb.1.new mv -f estwisedb.1.new estwisedb.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 ./estwise\.1 > estwise\.1\.new chmod 644 estwise.1.new mv -f estwise.1.new estwise.1 man --recode UTF-8 ./dba\.1 > dba\.1\.new chmod 644 dba.1.new mv -f dba.1.new dba.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 ./scanwise\.1 > scanwise\.1\.new chmod 644 scanwise.1.new mv -f scanwise.1.new scanwise.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 ./genewisedb\.1 > genewisedb\.1\.new chmod 644 genewisedb.1.new mv -f genewisedb.1.new genewisedb.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 ./genewise\.1 > genewise\.1\.new chmod 644 genewise.1.new mv -f genewise.1.new genewise.1 dh_perl dh_link dh_compress cd debian/wise chmod a-x usr/share/man/man1/genomewise.1 usr/share/man/man1/psw.1 usr/share/man/man1/estwisedb.1 usr/share/man/man1/promoterwise.1 usr/share/man/man1/estwise.1 usr/share/man/man1/dba.1 usr/share/man/man1/dnal.1 usr/share/man/man1/scanwise.1 usr/share/man/man1/scanwise_server.1 usr/share/man/man1/genewisedb.1 usr/share/man/man1/pswdb.1 usr/share/man/man1/genewise.1 usr/share/doc/wise/changelog.Debian gzip -9nf usr/share/man/man1/genomewise.1 usr/share/man/man1/psw.1 usr/share/man/man1/estwisedb.1 usr/share/man/man1/promoterwise.1 usr/share/man/man1/estwise.1 usr/share/man/man1/dba.1 usr/share/man/man1/dnal.1 usr/share/man/man1/scanwise.1 usr/share/man/man1/scanwise_server.1 usr/share/man/man1/genewisedb.1 usr/share/man/man1/pswdb.1 usr/share/man/man1/genewise.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/changelog.Debian usr/share/doc/wise-doc/dynamite.pdf usr/share/doc/wise-doc/wise2.pdf usr/share/doc/wise-doc/api.pdf gzip -9nf usr/share/doc/wise-doc/changelog.Debian usr/share/doc/wise-doc/dynamite.pdf usr/share/doc/wise-doc/wise2.pdf usr/share/doc/wise-doc/api.pdf cd '/build/buildd/wise-2.4.1' cd debian/wise-data chmod a-x usr/share/doc/wise-data/examples/basic_genomic.out usr/share/doc/wise-data/examples/wrong.hmm usr/share/doc/wise-data/examples/genewisedb-pfam.out usr/share/doc/wise-data/examples/scanwisep.out usr/share/doc/wise-data/examples/rrm.HMM usr/share/doc/wise-data/examples/HMM.ascii usr/share/doc/wise-data/examples/genewise-db.out usr/share/doc/wise-data/examples/hmm_genomic.out usr/share/doc/wise-data/examples/human.genomic usr/share/doc/wise-data/examples/estwise-db.out usr/share/doc/wise-data/examples/hmm_cdna.out usr/share/doc/wise-data/examples/genewise-db-lite.out usr/share/doc/wise-data/examples/basic_dna.out usr/share/doc/wise-data/examples/pswdb.out usr/share/doc/wise-data/examples/basic_cdna.out usr/share/doc/wise-data/examples/HMM.binary usr/share/doc/wise-data/examples/dna.db usr/share/doc/wise-data/changelog.Debian gzip -9nf usr/share/doc/wise-data/examples/basic_genomic.out usr/share/doc/wise-data/examples/wrong.hmm usr/share/doc/wise-data/examples/genewisedb-pfam.out usr/share/doc/wise-data/examples/scanwisep.out usr/share/doc/wise-data/examples/rrm.HMM usr/share/doc/wise-data/examples/HMM.ascii usr/share/doc/wise-data/examples/genewise-db.out usr/share/doc/wise-data/examples/hmm_genomic.out usr/share/doc/wise-data/examples/human.genomic usr/share/doc/wise-data/examples/estwise-db.out usr/share/doc/wise-data/examples/hmm_cdna.out usr/share/doc/wise-data/examples/genewise-db-lite.out usr/share/doc/wise-data/examples/basic_dna.out usr/share/doc/wise-data/examples/pswdb.out usr/share/doc/wise-data/examples/basic_cdna.out usr/share/doc/wise-data/examples/HMM.binary usr/share/doc/wise-data/examples/dna.db 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/x86_64-linux-gnu/perl5/5.20 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/x86_64-linux-gnu/perl5/5.20 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/x86_64-linux-gnu/perl5/5.20 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: not enabling -a because /CurrentlyBuilding exists dh_strip debug symbol extraction: all non-arch-all packages for this build platform amd64: wise dh_strip debug symbol extraction: packages to act on: wise dh_strip debug symbol extraction: ignored packages: Using buildid for compat level >= 9 dpkg-gencontrol: warning: -is is deprecated; it is without effect dpkg-gencontrol: warning: -ip is deprecated; it is without effect dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe /usr/bin/pkg_create_dbgsym: building ddeb package dpkg-deb: building package `wise-dbgsym' in `../wise-dbgsym_2.4.1-17_amd64.ddeb'. strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genewise strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/scanwise_server strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/dba strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/estwise strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/pswdb strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/dnal strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genewisedb strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genomewise strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/psw strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/scanwise strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/promoterwise strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/estwisedb 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/genewise debian/wise/usr/bin/scanwise_server debian/wise/usr/bin/dba debian/wise/usr/bin/estwise debian/wise/usr/bin/pswdb debian/wise/usr/bin/dnal debian/wise/usr/bin/genewisedb debian/wise/usr/bin/genomewise debian/wise/usr/bin/psw debian/wise/usr/bin/scanwise debian/wise/usr/bin/promoterwise debian/wise/usr/bin/estwisedb 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 dh_builddeb dpkg-deb --build debian/wise .. INFO: pkgstriptranslations version 121 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_2.4.1-17_amd64.deb'. dpkg-deb --build debian/wise-doc .. INFO: pkgstriptranslations version 121 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_2.4.1-17_all.deb'. dpkg-deb --build debian/wise-data .. INFO: pkgstriptranslations version 121 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_2.4.1-17_all.deb'. dpkg-genchanges -b -mUbuntu/amd64 Build Daemon >../wise_2.4.1-17_amd64.changes dpkg-genchanges: binary-only upload (no source code included) dpkg-source --after-build wise-2.4.1 dpkg-buildpackage: binary-only upload (no source included) ****************************************************************************** Build finished at 20141025-2348 Publishing debug debs. chroot-autobuild/build/buildd/wise_2.4.1-17_amd64.deb: new debian package, version 2.0. size 956720 bytes: control archive= 2076 bytes. 1798 bytes, 34 lines control 1742 bytes, 29 lines md5sums Package: wise Version: 2.4.1-17 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 9864 Depends: libc6 (>= 2.14), libglib2.0-0 (>= 2.12.0), wise-data (= 2.4.1-17) Suggests: wise-doc (= 2.4.1-17) Section: science Priority: optional Homepage: http://www.ebi.ac.uk/~birney/wise2/ Description: comparison of biopolymers, like 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_2.4.1-17_all.deb: new debian package, version 2.0. size 816518 bytes: control archive= 938 bytes. 572 bytes, 14 lines control 766 bytes, 11 lines md5sums Package: wise-doc Source: wise Version: 2.4.1-17 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 1311 Recommends: wise (= 2.4.1-17), 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_2.4.1-17_all.deb: new debian package, version 2.0. size 107208 bytes: control archive= 2336 bytes. 536 bytes, 14 lines control 4268 bytes, 61 lines md5sums Package: wise-data Source: wise Version: 2.4.1-17 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 245 Recommends: wise (= 2.4.1-17) 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_2.4.1-17_amd64.deb: drwxr-xr-x root/root 0 2014-10-25 23:48 ./ drwxr-xr-x root/root 0 2014-10-25 23:47 ./usr/ drwxr-xr-x root/root 0 2014-10-25 23:47 ./usr/share/ drwxr-xr-x root/root 0 2014-10-25 23:47 ./usr/share/doc/ drwxr-xr-x root/root 0 2014-10-25 23:47 ./usr/share/doc/wise/ -rw-r--r-- root/root 1507 2014-10-25 23:48 ./usr/share/doc/wise/changelog.Debian.gz -rw-r--r-- root/root 320 2008-01-14 17:38 ./usr/share/doc/wise/README.Debian -rw-r--r-- root/root 229 2014-09-23 11:00 ./usr/share/doc/wise/run-unit-test -rw-r--r-- root/root 1973 2007-07-01 20:46 ./usr/share/doc/wise/README -rw-r--r-- root/root 4219 2012-03-30 10:07 ./usr/share/doc/wise/copyright drwxr-xr-x root/root 0 2014-10-25 23:47 ./usr/share/man/ drwxr-xr-x root/root 0 2014-10-25 23:47 ./usr/share/man/man1/ -rw-r--r-- root/root 870 2014-10-25 23:47 ./usr/share/man/man1/dba.1.gz -rw-r--r-- root/root 579 2014-10-25 23:47 ./usr/share/man/man1/dnal.1.gz -rw-r--r-- root/root 628 2014-10-25 23:47 ./usr/share/man/man1/genomewise.1.gz -rw-r--r-- root/root 623 2014-10-25 23:47 ./usr/share/man/man1/scanwise.1.gz -rw-r--r-- root/root 619 2014-10-25 23:47 ./usr/share/man/man1/genewisedb.1.gz -rw-r--r-- root/root 607 2014-10-25 23:47 ./usr/share/man/man1/scanwise_server.1.gz -rw-r--r-- root/root 617 2014-10-25 23:47 ./usr/share/man/man1/estwisedb.1.gz -rw-r--r-- root/root 608 2014-10-25 23:47 ./usr/share/man/man1/pswdb.1.gz -rw-r--r-- root/root 708 2014-10-25 23:47 ./usr/share/man/man1/psw.1.gz -rw-r--r-- root/root 617 2014-10-25 23:47 ./usr/share/man/man1/genewise.1.gz -rw-r--r-- root/root 618 2014-10-25 23:47 ./usr/share/man/man1/estwise.1.gz -rw-r--r-- root/root 615 2014-10-25 23:47 ./usr/share/man/man1/promoterwise.1.gz drwxr-xr-x root/root 0 2014-10-25 23:48 ./usr/bin/ -rwxr-xr-x root/root 1893728 2014-10-25 23:48 ./usr/bin/genewise -rwxr-xr-x root/root 183120 2014-10-25 23:48 ./usr/bin/scanwise_server -rwxr-xr-x root/root 309944 2014-10-25 23:48 ./usr/bin/dba -rwxr-xr-x root/root 1889568 2014-10-25 23:48 ./usr/bin/estwise -rwxr-xr-x root/root 309992 2014-10-25 23:48 ./usr/bin/pswdb -rwxr-xr-x root/root 203368 2014-10-25 23:48 ./usr/bin/dnal -rwxr-xr-x root/root 1901984 2014-10-25 23:48 ./usr/bin/genewisedb -rwxr-xr-x root/root 342656 2014-10-25 23:48 ./usr/bin/genomewise -rwxr-xr-x root/root 305824 2014-10-25 23:48 ./usr/bin/psw -rwxr-xr-x root/root 445384 2014-10-25 23:48 ./usr/bin/scanwise -rwxr-xr-x root/root 367296 2014-10-25 23:48 ./usr/bin/promoterwise -rwxr-xr-x root/root 1893728 2014-10-25 23:48 ./usr/bin/estwisedb chroot-autobuild/build/buildd/wise-doc_2.4.1-17_all.deb: drwxr-xr-x root/root 0 2014-10-25 23:48 ./ drwxr-xr-x root/root 0 2014-10-25 23:47 ./usr/ drwxr-xr-x root/root 0 2014-10-25 23:47 ./usr/share/ drwxr-xr-x root/root 0 2014-10-25 23:47 ./usr/share/doc-base/ -rw-r--r-- root/root 314 2008-03-22 02:51 ./usr/share/doc-base/wise -rw-r--r-- root/root 363 2008-03-22 02:51 ./usr/share/doc-base/wise-dynamite -rw-r--r-- root/root 283 2009-04-16 12:39 ./usr/share/doc-base/wise-api drwxr-xr-x root/root 0 2014-10-25 23:47 ./usr/share/doc/ drwxr-xr-x root/root 0 2014-10-25 23:47 ./usr/share/doc/wise-doc/ -rw-r--r-- root/root 204821 2014-10-25 23:47 ./usr/share/doc/wise-doc/wise2.pdf.gz -rw-r--r-- root/root 212650 2014-10-25 23:47 ./usr/share/doc/wise-doc/dynamite.pdf.gz -rw-r--r-- root/root 1507 2014-10-25 23:48 ./usr/share/doc/wise-doc/changelog.Debian.gz -rw-r--r-- root/root 309519 2014-10-25 23:47 ./usr/share/doc/wise-doc/api.pdf.gz drwxr-xr-x root/root 0 2014-10-25 23:47 ./usr/share/doc/wise-doc/dynamite/ -rw-r--r-- root/root 107948 2014-10-25 23:47 ./usr/share/doc/wise-doc/dynamite/dynamite.html drwxr-xr-x root/root 0 2014-10-25 23:47 ./usr/share/doc/wise-doc/api/ -rw-r--r-- root/root 339713 2014-10-25 23:47 ./usr/share/doc/wise-doc/api/api.html drwxr-xr-x root/root 0 2014-10-25 23:47 ./usr/share/doc/wise-doc/wise2/ -rw-r--r-- root/root 118201 2014-10-25 23:47 ./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 chroot-autobuild/build/buildd/wise-data_2.4.1-17_all.deb: drwxr-xr-x root/root 0 2014-10-25 23:48 ./ drwxr-xr-x root/root 0 2014-10-25 23:47 ./usr/ drwxr-xr-x root/root 0 2014-10-25 23:47 ./usr/share/ drwxr-xr-x root/root 0 2014-10-25 23:47 ./usr/share/wise/ -rw-r--r-- root/root 3025 2001-06-18 13:59 ./usr/share/wise/gon200.bla -rw-r--r-- root/root 2074 2001-06-18 13:59 ./usr/share/wise/BLOSUM80.bla -rw-r--r-- root/root 4320 2002-05-21 14:36 ./usr/share/wise/wag75 -rw-r--r-- root/root 4243 2002-05-21 14:36 ./usr/share/wise/wag65 -rw-r--r-- root/root 3829 2002-04-30 10:25 ./usr/share/wise/gene.stat -rw-r--r-- root/root 4186 2002-05-21 14:36 ./usr/share/wise/wag55 -rw-r--r-- root/root 4418 2002-05-21 14:36 ./usr/share/wise/wag85 -rw-r--r-- root/root 2072 2001-06-18 13:59 ./usr/share/wise/BLOSUM30.bla -rw-r--r-- root/root 3209 2001-06-18 13:59 ./usr/share/wise/gon120.bla -rw-r--r-- root/root 5604 2001-06-18 13:59 ./usr/share/wise/pb.gf -rw-r--r-- root/root 2513 2001-06-18 13:59 ./usr/share/wise/gon350.bla -rw-r--r-- root/root 418 2001-06-18 13:59 ./usr/share/wise/codon.table -rw-r--r-- root/root 1655 2001-06-18 13:59 ./usr/share/wise/BLOSUM45.bla -rw-r--r-- root/root 2532 2001-06-18 13:59 ./usr/share/wise/gon160.bla -rw-r--r-- root/root 418 2002-12-11 17:53 ./usr/share/wise/codon.martian -rw-r--r-- root/root 15032 2001-06-18 13:59 ./usr/share/wise/worm.gf -rw-r--r-- root/root 703 2001-06-18 13:59 ./usr/share/wise/wise.2 -rw-r--r-- root/root 2711 2003-02-28 14:00 ./usr/share/wise/human.stats -rw-r--r-- root/root 2883 2001-06-18 13:59 ./usr/share/wise/idenity.bla -rw-r--r-- root/root 1655 2001-06-18 13:59 ./usr/share/wise/BLOSUM62.bla -rw-r--r-- root/root 2960 2001-06-18 14:44 ./usr/share/wise/methods -rw-r--r-- root/root 2115 2001-06-18 13:59 ./usr/share/wise/wise.per -rw-r--r-- root/root 10337 2001-06-18 13:59 ./usr/share/wise/cb.tmf -rw-r--r-- root/root 9057 2001-06-18 13:59 ./usr/share/wise/human.gf -rw-r--r-- root/root 2533 2001-06-18 13:59 ./usr/share/wise/gon250.bla -rw-r--r-- root/root 2650 2001-06-18 13:59 ./usr/share/wise/tm.pri -rw-r--r-- root/root 247 2001-06-18 13:59 ./usr/share/wise/aa.rnd -rw-r--r-- root/root 21690 2001-06-18 13:59 ./usr/share/wise/pombe.gf -rw-r--r-- root/root 9059 2001-06-18 13:59 ./usr/share/wise/human.gp drwxr-xr-x root/root 0 2014-10-25 23:47 ./usr/share/doc/ drwxr-xr-x root/root 0 2014-10-25 23:47 ./usr/share/doc/wise-data/ -rw-r--r-- root/root 1507 2014-10-25 23:48 ./usr/share/doc/wise-data/changelog.Debian.gz drwxr-xr-x root/root 0 2014-10-25 23:47 ./usr/share/doc/wise-data/examples/ -rw-r--r-- root/root 4391 2014-10-25 23:45 ./usr/share/doc/wise-data/examples/basic_cdna.out.gz -rw-r--r-- root/root 3946 2006-04-03 11:45 ./usr/share/doc/wise-data/examples/promoterwise.out -rw-r--r-- root/root 7580 2001-06-18 14:00 ./usr/share/doc/wise-data/examples/HMM.ascii.gz -rw-r--r-- root/root 452 2001-10-14 01:27 ./usr/share/doc/wise-data/examples/go.out -rw-r--r-- root/root 432 2001-06-18 14:00 ./usr/share/doc/wise-data/examples/short.dna -rw-r--r-- root/root 281 2003-04-14 09:47 ./usr/share/doc/wise-data/examples/wrong.out -rw-r--r-- root/root 6338 2001-06-18 14:00 ./usr/share/doc/wise-data/examples/wrong.hmm.gz -rw-r--r-- root/root 1964 2003-04-24 20:18 ./usr/share/doc/wise-data/examples/scanwisep.out.gz -rw-r--r-- root/root 60 2001-10-14 16:17 ./usr/share/doc/wise-data/examples/go.evi -rw-r--r-- root/root 4631 2014-10-25 23:45 ./usr/share/doc/wise-data/examples/basic_genomic.out.gz -rw-r--r-- root/root 2690 2014-10-25 23:45 ./usr/share/doc/wise-data/examples/genewisedb-pfam.out.gz -rw-r--r-- root/root 2201 2014-10-25 23:45 ./usr/share/doc/wise-data/examples/pswdb.out.gz -rw-r--r-- root/root 828 2003-02-28 13:47 ./usr/share/doc/wise-data/examples/pw.human -rw-r--r-- root/root 1314 2001-06-18 14:00 ./usr/share/doc/wise-data/examples/pep.fa -rw-r--r-- root/root 1843 2001-10-08 18:17 ./usr/share/doc/wise-data/examples/human.genomic.gz -rw-r--r-- root/root 4568 2001-06-18 14:00 ./usr/share/doc/wise-data/examples/basic_dna.out.gz -rw-r--r-- root/root 1637 2001-06-18 14:00 ./usr/share/doc/wise-data/examples/dna.db.gz -rw-r--r-- root/root 165 2001-06-18 14:00 ./usr/share/doc/wise-data/examples/short.pep -rw-r--r-- root/root 2958 2014-10-25 23:45 ./usr/share/doc/wise-data/examples/genewise-db-lite.out.gz -rw-r--r-- root/root 4525 2014-10-25 23:45 ./usr/share/doc/wise-data/examples/estwise-db.out.gz -rw-r--r-- root/root 5213 2001-06-18 14:00 ./usr/share/doc/wise-data/examples/HMM.binary.gz -rw-r--r-- root/root 5703 2001-06-18 14:00 ./usr/share/doc/wise-data/examples/rrm.HMM.gz -rw-r--r-- root/root 2956 2014-10-25 23:45 ./usr/share/doc/wise-data/examples/genewise-db.out.gz -rw-r--r-- root/root 895 2003-02-28 13:47 ./usr/share/doc/wise-data/examples/pw.mouse -rw-r--r-- root/root 559 2001-06-18 14:00 ./usr/share/doc/wise-data/examples/wrong_est.out -rw-r--r-- root/root 2319 2006-03-17 17:21 ./usr/share/doc/wise-data/examples/short.test -rw-r--r-- root/root 4589 2014-10-25 23:45 ./usr/share/doc/wise-data/examples/hmm_cdna.out.gz -rw-r--r-- root/root 4104 2014-10-25 23:45 ./usr/share/doc/wise-data/examples/hmm_genomic.out.gz -rw-r--r-- root/root 385 2001-06-18 14:00 ./usr/share/doc/wise-data/examples/road.pep -rwxr-xr-x root/root 2546 2014-10-25 23:47 ./usr/share/doc/wise-data/examples/testman.pl -rw-r--r-- root/root 4219 2012-03-30 10:07 ./usr/share/doc/wise-data/copyright wise_2.4.1-17_amd64.changes: Format: 1.8 Date: Tue, 23 Sep 2014 20:14:47 +0900 Source: wise Binary: wise wise-doc wise-data Architecture: amd64 all Version: 2.4.1-17 Distribution: vivid-proposed Urgency: medium Maintainer: Ubuntu/amd64 Build Daemon Changed-By: Charles Plessy Description: wise - comparison of biopolymers, like DNA and protein sequences wise-data - data files for the wise package wise-doc - documentation for the wise package Changes: wise (2.4.1-17) unstable; urgency=medium . * debian/tests/control: explicitly depend on wise. This avoids that ‘sadt’ skips the test when wise-doc is not installed. * debian/tests/run-unit-test: skip the first line of testman.pl, that misses a proper shebang and trigger a failure. * debian/control: shorten synopsis to less than 72 characters. * Conforms with Policy 3.9.6. Checksums-Sha1: 40d9238bb0b7cdb839b6b68b42461b1384aacb23 956720 wise_2.4.1-17_amd64.deb 1d8f8d1e5f8c9a02636de032bc30296dd11cd0df 816518 wise-doc_2.4.1-17_all.deb a389bbbc422bc80705f5d459c0a9a66062becb6b 107208 wise-data_2.4.1-17_all.deb Checksums-Sha256: 2cefeb04f834cb080ee75d254bbbaee4a57d76618485a1c6ba473a519d97e60c 956720 wise_2.4.1-17_amd64.deb 803a10b510bf346e2e0c0eec0dbd151fbdf36f305be8013a6b7c8340f143d8d8 816518 wise-doc_2.4.1-17_all.deb 74f188d1e3f5c04d4d3bf09e25d9efc503d23cff5c32aa7dc5615386e956dbe8 107208 wise-data_2.4.1-17_all.deb Files: 299935379b5e713d1dd2f39c5f50cedf 956720 science optional wise_2.4.1-17_amd64.deb f68f9f5b11a43211b658ee8173695ad6 816518 doc optional wise-doc_2.4.1-17_all.deb 9804cd6198b954a7434e43292e1c82fe 107208 doc optional wise-data_2.4.1-17_all.deb ****************************************************************************** Built successfully ****************************************************************************** Finished at 20141025-2348 Build needed 00:02:57, 143544k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-6502313'] Scanning for processes to kill in build /srv/home/buildd/build-PACKAGEBUILD-6502313/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-6502313'] Unmounting chroot for build PACKAGEBUILD-6502313... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-6502313'] Removing build PACKAGEBUILD-6502313