sbuild (Debian sbuild) 0.62.6 (07 Dec 2011) on build02.raspbian.lan ╔══════════════════════════════════════════════════════════════════════════════╗ ║ wise 2.4.1-10 (armhf) 04 May 2012 23:48 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: wise Version: 2.4.1-10 Source Version: 2.4.1-10 Distribution: testing Architecture: armhf I: NOTICE: Log filtering will replace 'build/wise-CAirVf/wise-2.4.1' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/wise-CAirVf' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/testing-armhf-sbuild-f30fed92-5fe1-4d1e-ae9d-94771c228405' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Update chroot │ └──────────────────────────────────────────────────────────────────────────────┘ Hit http://repo.raspbian.lan testing InRelease Hit http://repo.raspbian.lan testing/main Sources Hit http://repo.raspbian.lan testing/main armhf Packages Ign http://repo.raspbian.lan testing/main TranslationIndex Ign http://repo.raspbian.lan testing/main Translation-en Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Check APT ───────── Checking available source versions... Download source files with APT ────────────────────────────── Reading package lists... Building dependency tree... Reading state information... NOTICE: 'wise' packaging is maintained in the 'Svn' version control system at: svn://svn.debian.org/debian-med/trunk/packages/wise/trunk/ Need to get 3428 kB of source archives. Get:1 http://repo.raspbian.lan/raspbian/ testing/main wise 2.4.1-10 (dsc) [2084 B] Get:2 http://repo.raspbian.lan/raspbian/ testing/main wise 2.4.1-10 (tar) [3410 kB] Get:3 http://repo.raspbian.lan/raspbian/ testing/main wise 2.4.1-10 (diff) [15.7 kB] Fetched 3428 kB in 0s (9573 kB/s) Download complete and in download only mode Check arch ────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-nPNPbU/apt_archive/sbuild-build-depends-core-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install core build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/704 B of archives. After this operation, 0 B of additional disk space will be used. Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 10678 files and directories currently installed.) Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy.deb) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), quilt, texlive-latex-base, texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev Filtered Build-Depends: libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 8), quilt, texlive-latex-base, texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev dpkg-deb: building package `sbuild-build-depends-wise-dummy' in `/«BUILDDIR»/resolver-B4vdYz/apt_archive/sbuild-build-depends-wise-dummy.deb'. OK Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install wise build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: bsdmainutils debhelper diffstat docbook docbook-to-man ed file fontconfig-config gettext gettext-base ghostscript groff-base gs-cjk-resource gsfonts hevea html2text intltool-debian libavahi-client3 libavahi-common-data libavahi-common3 libcroco3 libcups2 libcupsimage2 libdb4.8 libdbus-1-3 libelf1 libexpat1 libffi5 libfontconfig1 libfreetype6 libgcrypt11 libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev libgnutls26 libgpg-error0 libgs9 libgs9-common libgssapi-krb5-2 libice6 libidn11 libijs-0.35 libjasper1 libjbig0 libjbig2dec0 libjpeg8 libk5crypto3 libkeyutils1 libkpathsea5 libkrb5-3 libkrb5support0 liblcms1 liblcms2-2 libmagic1 libnetpbm10 libopenjpeg2 libp11-kit0 libpaper-utils libpaper1 libpcre3 libpcre3-dev libpcrecpp0 libpipeline1 libpng12-0 libpoppler13 libpopt0 libsm6 libsp1c2 libsqlite3-0 libssl1.0.0 libtasn1-3 libtiff4 libunistring0 libx11-6 libx11-data libxau6 libxaw7 libxcb1 libxdmcp6 libxext6 libxml2 libxmu6 libxpm4 libxt6 luatex man-db mime-support netpbm ocaml-base-nox pkg-config po-debconf python python-minimal python2.7 python2.7-minimal quilt sgml-base sgml-data sp tex-common texlive-base texlive-binaries texlive-common texlive-doc-base texlive-extra-utils texlive-latex-base ttf-dejavu-core x11-common xml-core zlib1g-dev Suggested packages: wamerican wordlist whois vacation dh-make psgml docbook-dsssl docbook-xml docbook-defguide gettext-doc ghostscript-cups ghostscript-x hpijs groff fonts-ipafont-mincho fonts-ipafont-gothic ttf-arphic-ukai ttf-arphic-uming fonts-unfonts-core hevea-doc cups-common rng-tools libglib2.0-doc krb5-doc krb5-user libjasper-runtime liblcms-utils liblcms2-utils less www-browser libmail-box-perl python-doc python-tk python2.7-doc binfmt-support procmail graphviz default-mta mail-transport-agent sgml-base-doc perlsgml doc-html-w3 opensp libxml2-utils doc-base perl-tk xpdf-reader pdf-viewer gv postscript-viewer dvidvi fragmaster latexmk Recommended packages: curl wget lynx-cur autopoint cmap-adobe-japan1 cmap-adobe-cns1 cmap-adobe-gb1 cmap-adobe-korea1 cmap-adobe-japan2 dbus shared-mime-info fonts-droid krb5-locales poppler-data texlive-luatex libmail-sendmail-perl lmodern purifyeps xindy lacheck texlive-latex-base-doc The following NEW packages will be installed: bsdmainutils debhelper diffstat docbook docbook-to-man ed file fontconfig-config gettext gettext-base ghostscript groff-base gs-cjk-resource gsfonts hevea html2text intltool-debian libavahi-client3 libavahi-common-data libavahi-common3 libcroco3 libcups2 libcupsimage2 libdb4.8 libdbus-1-3 libelf1 libexpat1 libffi5 libfontconfig1 libfreetype6 libgcrypt11 libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev libgnutls26 libgpg-error0 libgs9 libgs9-common libgssapi-krb5-2 libice6 libidn11 libijs-0.35 libjasper1 libjbig0 libjbig2dec0 libjpeg8 libk5crypto3 libkeyutils1 libkpathsea5 libkrb5-3 libkrb5support0 liblcms1 liblcms2-2 libmagic1 libnetpbm10 libopenjpeg2 libp11-kit0 libpaper-utils libpaper1 libpcre3 libpcre3-dev libpcrecpp0 libpipeline1 libpng12-0 libpoppler13 libpopt0 libsm6 libsp1c2 libsqlite3-0 libssl1.0.0 libtasn1-3 libtiff4 libunistring0 libx11-6 libx11-data libxau6 libxaw7 libxcb1 libxdmcp6 libxext6 libxml2 libxmu6 libxpm4 libxt6 luatex man-db mime-support netpbm ocaml-base-nox pkg-config po-debconf python python-minimal python2.7 python2.7-minimal quilt sbuild-build-depends-wise-dummy sgml-base sgml-data sp tex-common texlive-base texlive-binaries texlive-common texlive-doc-base texlive-extra-utils texlive-latex-base ttf-dejavu-core x11-common xml-core zlib1g-dev 0 upgraded, 112 newly installed, 0 to remove and 0 not upgraded. Need to get 1584 kB/76.2 MB of archives. After this operation, 183 MB of additional disk space will be used. Get:1 http://repo.raspbian.lan/raspbian/ testing/main texlive-extra-utils all 2009-10 [1584 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1584 kB in 0s (8493 kB/s) Selecting previously unselected package libpcre3:armhf. (Reading database ... 10678 files and directories currently installed.) Unpacking libpcre3:armhf (from .../libpcre3_1%3a8.30-4_armhf.deb) ... Selecting previously unselected package libpipeline1:armhf. Unpacking libpipeline1:armhf (from .../libpipeline1_1.2.1-1_armhf.deb) ... Selecting previously unselected package libpopt0:armhf. Unpacking libpopt0:armhf (from .../libpopt0_1.16-3_armhf.deb) ... Selecting previously unselected package libssl1.0.0:armhf. Unpacking libssl1.0.0:armhf (from .../libssl1.0.0_1.0.1b-1_armhf.deb) ... Selecting previously unselected package libgpg-error0:armhf. 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Unpacking libkpathsea5 (from .../libkpathsea5_2009-12_armhf.deb) ... Selecting previously unselected package texlive-binaries. Unpacking texlive-binaries (from .../texlive-binaries_2009-12_armhf.deb) ... Selecting previously unselected package texlive-base. Unpacking texlive-base (from .../texlive-base_2009-15_all.deb) ... Selecting previously unselected package ocaml-base-nox. Unpacking ocaml-base-nox (from .../ocaml-base-nox_3.12.1-2_armhf.deb) ... Selecting previously unselected package hevea. Unpacking hevea (from .../archives/hevea_1.10-14_all.deb) ... Selecting previously unselected package libelf1. Unpacking libelf1 (from .../libelf1_0.152-1+rpi1_armhf.deb) ... Selecting previously unselected package libglib2.0-data. Unpacking libglib2.0-data (from .../libglib2.0-data_2.32.0-4_all.deb) ... Selecting previously unselected package libglib2.0-bin. Unpacking libglib2.0-bin (from .../libglib2.0-bin_2.32.0-4_armhf.deb) ... Selecting previously unselected package libpcre3-dev. Unpacking libpcre3-dev (from .../libpcre3-dev_1%3a8.30-4_armhf.deb) ... Selecting previously unselected package pkg-config. Unpacking pkg-config (from .../pkg-config_0.26-1_armhf.deb) ... Selecting previously unselected package zlib1g-dev:armhf. Unpacking zlib1g-dev:armhf (from .../zlib1g-dev_1%3a1.2.6.dfsg-2_armhf.deb) ... Selecting previously unselected package libglib2.0-dev. Unpacking libglib2.0-dev (from .../libglib2.0-dev_2.32.0-4_armhf.deb) ... Selecting previously unselected package quilt. Unpacking quilt (from .../archives/quilt_0.60-2_all.deb) ... Selecting previously unselected package texlive-extra-utils. Unpacking texlive-extra-utils (from .../texlive-extra-utils_2009-10_all.deb) ... Selecting previously unselected package texlive-latex-base. Unpacking texlive-latex-base (from .../texlive-latex-base_2009-15_all.deb) ... Selecting previously unselected package sbuild-build-depends-wise-dummy. Unpacking sbuild-build-depends-wise-dummy (from .../sbuild-build-depends-wise-dummy.deb) ... Setting up libpcre3:armhf (1:8.30-4) ... Setting up libpipeline1:armhf (1.2.1-1) ... Setting up libpopt0:armhf (1.16-3) ... Setting up libssl1.0.0:armhf (1.0.1b-1) ... Setting up libgpg-error0:armhf (1.10-3) ... Setting up libgcrypt11:armhf (1.5.0-3) ... Setting up libp11-kit0:armhf (0.12-3) ... Setting up libtasn1-3:armhf (2.12-1) ... Setting up libgnutls26:armhf (2.12.18-1) ... Setting up libkrb5support0:armhf (1.10+dfsg~beta1-2) ... Setting up libk5crypto3:armhf (1.10+dfsg~beta1-2) ... Setting up libkeyutils1:armhf (1.5.2-2) ... Setting up libkrb5-3:armhf (1.10+dfsg~beta1-2) ... Setting up libgssapi-krb5-2:armhf (1.10+dfsg~beta1-2) ... Setting up libidn11:armhf (1.24-2) ... Setting up libmagic1:armhf (5.11-1) ... Setting up libsqlite3-0:armhf (3.7.11-2) ... Setting up libxml2:armhf (2.7.8.dfsg-9) ... Setting up libavahi-common-data:armhf (0.6.31-1) ... Setting up libavahi-common3:armhf (0.6.31-1) ... Setting up libdbus-1-3:armhf (1.5.12-1) ... Setting up libavahi-client3:armhf (0.6.31-1) ... Setting up libffi5:armhf (3.0.10-3+b3) ... Setting up libglib2.0-0:armhf (2.32.0-4) ... No schema files found: doing nothing. Setting up libcroco3:armhf (0.6.5-1) ... Setting up libcups2:armhf (1.5.2-5) ... Setting up libjpeg8:armhf (8d-1) ... Setting up libpng12-0:armhf (1.2.49-1) ... Setting up libjbig0:armhf (2.0-2) ... Setting up libtiff4:armhf (3.9.6-5) ... Setting up libcupsimage2:armhf (1.5.2-5) ... Setting up libexpat1:armhf (2.1.0-1) ... Setting up libfreetype6:armhf (2.4.9-1) ... Setting up ttf-dejavu-core (2.33-2) ... Setting up fontconfig-config (2.8.0-3.1) ... Setting up libfontconfig1:armhf (2.8.0-3.1) ... Setting up x11-common (1:7.6+12) ... All runlevel operations denied by policy invoke-rc.d: policy-rc.d denied execution of start. Setting up libice6:armhf (2:1.0.8-2) ... Setting up libjasper1:armhf (1.900.1-13) ... Setting up libpcrecpp0:armhf (1:8.30-4) ... Setting up libsm6:armhf (2:1.2.1-2) ... Setting up libunistring0:armhf (0.9.3-5) ... Setting up libxau6:armhf (1:1.0.7-1) ... Setting up libxdmcp6:armhf (1:1.1.1-1) ... Setting up libxcb1:armhf (1.8.1-1) ... Setting up libx11-data (2:1.4.4-4) ... Setting up libx11-6:armhf (2:1.4.4-4) ... Setting up libxext6:armhf (2:1.3.1-2) ... Setting up libxt6:armhf (1:1.1.3-1) ... Setting up libxmu6:armhf (2:1.1.1-1) ... Setting up libxpm4:armhf (1:3.5.10-1) ... Setting up libxaw7:armhf (2:1.0.10-2) ... Setting up libdb4.8:armhf (4.8.30-11) ... Setting up bsdmainutils (9.0.1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode. update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode. Setting up groff-base (1.21-7) ... Setting up man-db (2.6.1-2) ... Building database of manual pages ... Setting up file (5.11-1) ... Setting up gettext-base (0.18.1.1-5+rpi1) ... Setting up mime-support (3.52-1) ... update-alternatives: using /usr/bin/see to provide /usr/bin/view (view) in auto mode. Setting up python2.7-minimal (2.7.2-8) ... Setting up python2.7 (2.7.2-8) ... Setting up python-minimal (2.7.2-10) ... Setting up python (2.7.2-10) ... Setting up html2text (1.3.2a-15) ... Setting up gettext (0.18.1.1-5+rpi1) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu2) ... Setting up debhelper (9.20120419) ... Setting up diffstat (1.55-2) ... Setting up sgml-base (1.26+nmu1) ... Setting up xml-core (0.13) ... Setting up sgml-data (2.0.6) ... Setting up docbook (4.5-4) ... Setting up libsp1c2 (1.3.4-1.2.1-47.1) ... Setting up sp (1.3.4-1.2.1-47.1) ... Setting up docbook-to-man (1:2.0.0-29) ... Setting up ed (1.6-1) ... Setting up libijs-0.35 (0.35-8) ... Setting up libjbig2dec0 (0.11+20120125-1) ... Setting up liblcms2-2 (2.2+git20110628-2.1) ... Setting up libpaper1 (1.1.24+nmu1) ... Creating config file /etc/papersize with new version Setting up libgs9-common (9.05~dfsg-4) ... Setting up gsfonts (1:8.11+urwcyr1.0.7~pre44-4.2) ... Setting up libnetpbm10 (2:10.0-15) ... Setting up netpbm (2:10.0-15) ... Setting up tex-common (2.10) ... Creating config file /etc/texmf/texmf.d/05TeXMF.cnf with new version Creating config file /etc/texmf/texmf.d/15Plain.cnf with new version Creating config file /etc/texmf/texmf.d/45TeXinputs.cnf with new version Creating config file /etc/texmf/texmf.d/55Fonts.cnf with new version Creating config file /etc/texmf/texmf.d/65BibTeX.cnf with new version Creating config file /etc/texmf/texmf.d/75DviPS.cnf with new version Creating config file /etc/texmf/texmf.d/80DVIPDFMx.cnf with new version Creating config file /etc/texmf/texmf.d/85Misc.cnf with new version Creating config file /etc/texmf/texmf.d/90TeXDoc.cnf with new version Creating config file /etc/texmf/texmf.d/95NonPath.cnf with new version Creating config file /etc/texmf/updmap.d/00updmap.cfg with new version Creating config file /etc/texmf/texmf.cnf with new version Running mktexlsr. This may take some time... done. texlive-base is not ready, delaying updmap-sys call texlive-base is not ready, skipping fmtutil-sys --all call Setting up texlive-common (2009-15) ... Setting up texlive-doc-base (2009-2) ... Setting up libpaper-utils (1.1.24+nmu1) ... Setting up liblcms1 (1.19.dfsg-1) ... Setting up libopenjpeg2 (1.3+dfsg-4) ... Setting up libpoppler13 (0.16.7-3) ... Setting up luatex (0.70.1-3) ... texlive-base is not ready, cannot create formats Setting up libkpathsea5 (2009-12) ... Setting up texlive-binaries (2009-12) ... 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 ocaml-base-nox (3.12.1-2) ... Setting up libelf1 (0.152-1+rpi1) ... Setting up libglib2.0-data (2.32.0-4) ... Setting up libglib2.0-bin (2.32.0-4) ... Setting up libpcre3-dev (1:8.30-4) ... Setting up pkg-config (0.26-1) ... Setting up zlib1g-dev:armhf (1:1.2.6.dfsg-2) ... Setting up libglib2.0-dev (2.32.0-4) ... Setting up quilt (0.60-2) ... Processing triggers for tex-common ... Running mktexlsr. This may take some time... done. Setting up texlive-base (2009-15) ... Creating config file /etc/texmf/dvips/config/config.ps with new version Creating config file /etc/texmf/tex/generic/config/pdftexconfig.tex with new version Creating config file /etc/texmf/dvipdfmx/dvipdfmx.cfg with new version Creating config file /etc/texmf/xdvi/XDvi with new version Running mktexlsr. This may take some time... done. Building format(s) --all --cnffile /etc/texmf/fmt.d/10texlive-base.cnf. This may take some time... done. Processing triggers for tex-common ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building e-tex based formats --byhyphen /var/lib/texmf/tex/generic/config/language.def. This may take some time... done. Setting up texlive-latex-base (2009-15) ... 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. Setting up texlive-extra-utils (2009-10) ... Processing triggers for tex-common ... Running mktexlsr. This may take some time... done. Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Setting up libgs9 (9.05~dfsg-4) ... Setting up ghostscript (9.05~dfsg-4) ... Setting up gs-cjk-resource (1.20100103-3) ... Setting up hevea (1.10-14) ... Processing triggers for tex-common ... Running mktexlsr. This may take some time... done. Setting up sbuild-build-depends-wise-dummy (0.invalid.0) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.2.0-2-mx5 armhf (armv7l) Toolchain package versions: binutils_2.22-6 dpkg-dev_1.16.2 g++-4.6_4.6.3-1.1+rpi2 gcc-4.6_4.6.3-1.1+rpi2 libc6-dev_2.13-30 libstdc++6_4.7.0-1.1+rpi libstdc++6-4.6-dev_4.6.3-1.1+rpi2 linux-libc-dev_3.2.12-1 Package versions: apt_0.8.15.10 base-files_6.7 base-passwd_3.5.24 bash_4.2-2 binutils_2.22-6 bsdmainutils_9.0.1 bsdutils_1:2.20.1-4 build-essential_11.5+b1 bzip2_1.0.6-1 coreutils_8.13-3.1 cpp_4:4.6.2-4 cpp-4.6_4.6.3-1.1+rpi2 dash_0.5.7-3 debconf_1.5.42 debfoster_2.7-1.1 debhelper_9.20120419 debian-archive-keyring_2010.08.28 debianutils_4.3 diffstat_1.55-2 diffutils_1:3.2-2 docbook_4.5-4 docbook-to-man_1:2.0.0-29 dpkg_1.16.2 dpkg-dev_1.16.2 e2fslibs_1.42.2-2 e2fsprogs_1.42.2-2 ed_1.6-1 fakeroot_1.18.3-1 file_5.11-1 findutils_4.4.2-4 fontconfig-config_2.8.0-3.1 g++_4:4.6.2-4 g++-4.6_4.6.3-1.1+rpi2 gcc_4:4.6.2-4 gcc-4.4-base_4.4.7-1 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6_4.6.3-1.1+rpi2 gcc-4.6-base_4.6.3-1.1+rpi2 gcc-4.7-base_4.7.0-1.1+rpi gettext_0.18.1.1-5+rpi1 gettext-base_0.18.1.1-5+rpi1 ghostscript_9.05~dfsg-4 gnupg_1.4.12-4 gpgv_1.4.12-4 grep_2.11-3 groff-base_1.21-7 gs-cjk-resource_1.20100103-3 gsfonts_1:8.11+urwcyr1.0.7~pre44-4.2 gzip_1.4-5 hevea_1.10-14 hostname_3.11 html2text_1.3.2a-15 initscripts_2.88dsf-22.1 insserv_1.14.0-3 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libavahi-client3_0.6.31-1 libavahi-common-data_0.6.31-1 libavahi-common3_0.6.31-1 libblkid1_2.20.1-4 libbz2-1.0_1.0.6-1 libc-bin_2.13-30 libc-dev-bin_2.13-30 libc6_2.13-30 libc6-dev_2.13-30 libclass-isa-perl_0.36-3 libcomerr2_1.42.2-2 libcroco3_0.6.5-1 libcups2_1.5.2-5 libcupsimage2_1.5.2-5 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdbus-1-3_1.5.12-1 libdpkg-perl_1.16.2 libelf1_0.152-1+rpi1 libexpat1_2.1.0-1 libffi5_3.0.10-3+b3 libfile-fcntllock-perl_0.14-1 libfontconfig1_2.8.0-3.1 libfreetype6_2.4.9-1 libgc1c2_1:7.1-8 libgcc1_1:4.7.0-1.1+rpi libgcrypt11_1.5.0-3 libgdbm3_1.8.3-10 libglib2.0-0_2.32.0-4 libglib2.0-bin_2.32.0-4 libglib2.0-data_2.32.0-4 libglib2.0-dev_2.32.0-4 libgmp10_2:5.0.4+dfsg-1 libgnutls26_2.12.18-1 libgomp1_4.7.0-1.1+rpi libgpg-error0_1.10-3 libgs9_9.05~dfsg-4 libgs9-common_9.05~dfsg-4 libgssapi-krb5-2_1.10+dfsg~beta1-2 libice6_2:1.0.8-2 libidn11_1.24-2 libijs-0.35_0.35-8 libjasper1_1.900.1-13 libjbig0_2.0-2 libjbig2dec0_0.11+20120125-1 libjpeg8_8d-1 libk5crypto3_1.10+dfsg~beta1-2 libkeyutils1_1.5.2-2 libkpathsea5_2009-12 libkrb5-3_1.10+dfsg~beta1-2 libkrb5support0_1.10+dfsg~beta1-2 liblcms1_1.19.dfsg-1 liblcms2-2_2.2+git20110628-2.1 liblocale-gettext-perl_1.05-7 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.11-1 libmount1_2.20.1-4 libmpc2_0.9-4 libmpfr4_3.1.0-4 libncurses5_5.9-6 libncursesw5_5.9-6 libnetpbm10_2:10.0-15 libopenjpeg2_1.3+dfsg-4 libp11-kit0_0.12-3 libpam-modules_1.1.3-7 libpam-modules-bin_1.1.3-7 libpam-runtime_1.1.3-7 libpam0g_1.1.3-7 libpaper-utils_1.1.24+nmu1 libpaper1_1.1.24+nmu1 libpcre3_1:8.30-4 libpcre3-dev_1:8.30-4 libpcrecpp0_1:8.30-4 libpipeline1_1.2.1-1 libpng12-0_1.2.49-1 libpoppler13_0.16.7-3 libpopt0_1.16-3 libreadline6_6.2-8 libselinux1_2.1.9-2 libsemanage-common_2.1.6-2 libsemanage1_2.1.6-2 libsepol1_2.1.4-1 libslang2_2.2.4-7 libsm6_2:1.2.1-2 libsp1c2_1.3.4-1.2.1-47.1 libsqlite3-0_3.7.11-2 libss2_1.42.2-2 libssl1.0.0_1.0.1b-1 libstdc++6_4.7.0-1.1+rpi libstdc++6-4.6-dev_4.6.3-1.1+rpi2 libswitch-perl_2.16-2 libtasn1-3_2.12-1 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtiff4_3.9.6-5 libtimedate-perl_1.2000-1 libtinfo5_5.9-6 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libustr-1.0-1_1.0.4-2 libuuid1_2.20.1-4 libx11-6_2:1.4.4-4 libx11-data_2:1.4.4-4 libxau6_1:1.0.7-1 libxaw7_2:1.0.10-2 libxcb1_1.8.1-1 libxdmcp6_1:1.1.1-1 libxext6_2:1.3.1-2 libxml2_2.7.8.dfsg-9 libxmu6_2:1.1.1-1 libxpm4_1:3.5.10-1 libxt6_1:1.1.3-1 linux-libc-dev_3.2.12-1 login_1:4.1.5-1 lsb-base_4.1+Debian0 luatex_0.70.1-3 make_3.81-8.1 man-db_2.6.1-2 mawk_1.3.3-17 mime-support_3.52-1 mount_2.20.1-4 multiarch-support_2.13-30 ncurses-base_5.9-6 ncurses-bin_5.9-6 netpbm_2:10.0-15 ocaml-base-nox_3.12.1-2 passwd_1:4.1.5-1 patch_2.6.1-3 perl_5.14.2-9 perl-base_5.14.2-9 perl-modules_5.14.2-9 pkg-config_0.26-1 po-debconf_1.0.16+nmu2 python_2.7.2-10 python-minimal_2.7.2-10 python2.7_2.7.2-8 python2.7-minimal_2.7.2-8 quilt_0.60-2 readline-common_6.2-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-wise-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sgml-base_1.26+nmu1 sgml-data_2.0.6 sp_1.3.4-1.2.1-47.1 sysv-rc_2.88dsf-22.1 sysvinit_2.88dsf-22.1 sysvinit-utils_2.88dsf-22.1 tar_1.26-4 tex-common_2.10 texlive-base_2009-15 texlive-binaries_2009-12 texlive-common_2009-15 texlive-doc-base_2009-2 texlive-extra-utils_2009-10 texlive-latex-base_2009-15 ttf-dejavu-core_2.33-2 tzdata_2012b-1 ucf_3.0025+nmu3 util-linux_2.20.1-4 x11-common_1:7.6+12 xml-core_0.13 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.6.dfsg-2 zlib1g-dev_1:1.2.6.dfsg-2 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error gpgv: Signature made Fri Mar 30 10:32:28 2012 UTC using RSA key ID 2295D502 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./wise_2.4.1-10.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: applying wise_2.4.1-10.diff.gz Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── HOME=/sbuild-nonexistent LOGNAME=buildd PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/X11R6/bin:/usr/games SCHROOT_CHROOT_NAME=testing-armhf-sbuild SCHROOT_COMMAND=env SCHROOT_GID=108 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=testing-armhf-sbuild-f30fed92-5fe1-4d1e-ae9d-94771c228405 SCHROOT_UID=106 SCHROOT_USER=buildd SHELL=/bin/sh TERM=xterm USER=buildd dpkg-buildpackage ───────────────── dpkg-buildpackage: source package wise dpkg-buildpackage: source version 2.4.1-10 dpkg-source --before-build wise-2.4.1 dpkg-buildpackage: host architecture armhf fakeroot debian/rules clean dh clean --with quilt dh_testdir dh_auto_clean dh_quilt_unpatch quilt --quiltrc /dev/null pop -a || test $? = 2 No patch removed rm -rf .pc debian/rules override_dh_clean make[1]: Entering directory `/«PKGBUILDDIR»' /usr/bin/make -C src clean make[2]: Entering directory `/«PKGBUILDDIR»/src' cd external ; /usr/bin/make clean make[3]: Entering directory `/«PKGBUILDDIR»/src/external' (cd mott; make clean) make[4]: Entering directory `/«PKGBUILDDIR»/src/external/mott' rm -f *.[oa] make[4]: Leaving directory `/«PKGBUILDDIR»/src/external/mott' make[3]: Leaving directory `/«PKGBUILDDIR»/src/external' if test -d dynlibsrc; then cd dynlibsrc ; rm -f *.[oa]; fi if test -d models; then cd models ; rm -f *.[oa]; fi if test -d base; then cd base ; rm -f *.[oa]; fi if test -d socket; then cd socket ; rm -f *.[oa]; fi if test -d dnaindex; then cd dnaindex ; rm -f *.[oa]; fi if test -d network; then cd network ; rm -f *.[oa]; fi if test -d dyc; then cd dyc ; rm -f *.[oa]; fi if test -d HMMer2; then cd HMMer2 ; rm -f *.[oa]; fi if test -d perl; then cd perl/Wise2/libs ; rm -f *.[oa]; fi if test -x perl/Wise2/Makefile; then cd perl/Wise2/ ; /usr/bin/make clean; fi if test -d oldbin; then rm -rf oldbin; fi if test -d bin; then echo 'moving binaries to oldbin'; mv -f bin oldbin; fi make[2]: Leaving directory `/«PKGBUILDDIR»/src' /usr/bin/make -C debian/manpages.d clean make[2]: Entering directory `/«PKGBUILDDIR»/debian/manpages.d' rm -f dba.1 dnal.1 estwise.1 estwisedb.1 genewise.1 genewisedb.1 genomewise.1 promoterwise.1 psw.1 pswdb.1 scanwise.1 scanwise_server.1 make[2]: Leaving directory `/«PKGBUILDDIR»/debian/manpages.d' rm -f -r src/oldbin for i in dba psw dnal genomewise pswdb scanwise estwise genewise sywise genewisedb promoterwise pseudowise estwisedb; do rm -f src/modules/$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/*.debhelper.log rm -f debian/files find . \( \( -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} \; \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} \; \) \) rm -f *-stamp make[1]: Leaving directory `/«PKGBUILDDIR»' debian/rules build-arch dh build-arch --with quilt dh_testdir -a dh_quilt_patch -a quilt --quiltrc /dev/null push -a || test $? = 2 Applying patch 01_welcome-csh.patch patching file src/makefile patching file src/welcome.csh Applying patch 02_isnumber.patch patching file src/models/phasemodel.c Applying patch 03_doc-nodycache.patch patching file docs/wise2.tex Applying patch 04_wise2-pdflatex-update.patch patching file docs/wise2.tex Applying patch 05_glib2.patch patching file src/makefile patching file src/snp/makefile patching file src/corba/makefile patching file src/models/makefile patching file src/dnaindex/makefile patching file src/dnaindex/assembly/makefile patching file src/dynlibsrc/makefile patching file src/network/makefile patching file src/other_programs/makefile Applying patch 06_getline.patch patching file src/HMMer2/sqio.c Applying patch 07_ld--as-needed.patch patching file src/models/makefile Now at patch 07_ld--as-needed.patch dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory `/«PKGBUILDDIR»' /usr/bin/make -C src all make[2]: Entering directory `/«PKGBUILDDIR»/src' (cd base ; /usr/bin/make CC="cc" CFLAGS="-c -O3 `pkg-config --cflags glib-2.0`" libwisebase.a ) make[3]: Entering directory `/«PKGBUILDDIR»/src/base' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include wiseconfig.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include wisestring.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include wiseerror.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include wisememman.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include wisefile.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include wiserandom.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include wisetime.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include wiseoverlay.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include wisestreaminterface.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include commandline.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/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 `/«PKGBUILDDIR»/src/base' (cd HMMer2 ; /usr/bin/make CC="cc" CFLAGS="-c -O3 `pkg-config --cflags glib-2.0`" libhmmer.a ) make[3]: Entering directory `/«PKGBUILDDIR»/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c alphabet.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c core_algorithms.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c debug.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c emit.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c emulation.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c histogram.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c hmmio.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c mathsupport.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c masks.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c misc.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c modelmakers.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c plan7.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c plan9.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c prior.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c tophits.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c trace.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c aligneval.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c alignio.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c cluster.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c dayhoff.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c file.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c getopt.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c gnuregex.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c interleaved.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c iupac.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c msf.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c revcomp.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c selex.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c sqerror.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c sqio.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c sre_ctype.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c sre_math.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c sre_string.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c stack.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c translate.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c types.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/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 `/«PKGBUILDDIR»/src/HMMer2' (cd dynlibsrc ; /usr/bin/make CC="cc" CFLAGS="-c -O3 `pkg-config --cflags glib-2.0`" libdyna.a ) make[3]: Entering directory `/«PKGBUILDDIR»/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ packaln.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ aln.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ dnamatrix.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ probability.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ alnrange.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ alnconvert.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ basematrix.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ shattermatrix.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ matrixdebug.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ dpenvelope.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ dbsearchimpl.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ dprunimpl.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ complexsequence.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ complexevalset.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ complexconsensi.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ sequence.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ sequencestream.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ seqalign.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ hitlist.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ hsp.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ hspstream.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ codon.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ compmat.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ codonmatrix.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ codonmapper.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ sequencedb.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ hscore.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ seqlookup.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ arrayseqlookup.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ genericindexresult.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ linkedlist_lookpos.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ singlenumberspace.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ histogram.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ searchstatinterface.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ searchstatlookup.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ proteindb.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ protein.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ pairbase.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ pairbaseseq.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ genomicdb.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ randommodel.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ randomdb.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ genomic.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ cdna.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ cdnadb.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ dna.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ embl.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ genomicregion.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ gene.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ transcript.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ translation.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ btcanvas.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ asciibtcanvas.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/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 `/«PKGBUILDDIR»/src/dynlibsrc' (cd dynlibsrc ; /usr/bin/make CC="cc" CFLAGS="-c -O3 `pkg-config --cflags glib-2.0`" libdyna_glib.a ) make[3]: Entering directory `/«PKGBUILDDIR»/src/dynlibsrc' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ subseqhash.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ intallocator.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ proteinstreamedindex.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ shadowseq.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ shadowseqindex.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ hsphandler.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ hspscaninterface.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ hsp2hitscan.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ hsplookupscan.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ hsplookupthreaded.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ hspthreadeddb.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ hspscanruntime.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ hsptwohitscan.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ proteinindexcons.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ dnaindexcons.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/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 `/«PKGBUILDDIR»/src/dynlibsrc' (cd external ; /usr/bin/make CC="cc" CFLAGS="-c -O3 `pkg-config --cflags glib-2.0`" all ) make[3]: Entering directory `/«PKGBUILDDIR»/src/external' (cd mott; make CC="cc" CFLAGS="-c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include " all) make[4]: Entering directory `/«PKGBUILDDIR»/src/external/mott' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c -o mott_api.o mott_api.c mott_api.c: In function 'InitPvaluesMott': mott_api.c:64:3: warning: incompatible implicit declaration of built-in function 'free' [enabled by default] mott_api.c: In function 'SW_PValueMott': mott_api.c:104:7: warning: incompatible implicit declaration of built-in function 'free' [enabled by default] mott_api.c: In function 'KarlinAltschulStatistics2': mott_api.c:144:5: warning: incompatible implicit declaration of built-in function 'free' [enabled by default] mott_api.c:155:5: warning: incompatible implicit declaration of built-in function 'free' [enabled by default] mott_api.c: In function 'GetHistogram': mott_api.c:179:16: warning: incompatible implicit declaration of built-in function 'calloc' [enabled by default] mott_api.c: In function 'RobinsonResidueFrequencies2': mott_api.c:230:27: warning: incompatible implicit declaration of built-in function 'calloc' [enabled by default] cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -c -o gaplib.o gaplib.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/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 `/«PKGBUILDDIR»/src/external/mott' make[3]: Leaving directory `/«PKGBUILDDIR»/src/external' (cd socket ; /usr/bin/make CC="cc" CFLAGS="-c -O3 `pkg-config --cflags glib-2.0`" libwisesocket.a ) make[3]: Entering directory `/«PKGBUILDDIR»/src/socket' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ functionserver.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ functionclient.c functionclient.dy: In function 'Wise2_new_FunctionProxyCoordinator': functionclient.dy:193:3: warning: passing argument 2 of 'connect' from incompatible pointer type [enabled by default] /usr/include/arm-linux-gnueabihf/sys/socket.h:129:12: note: expected 'const struct sockaddr *' but argument is of type 'struct sockaddr_in *' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ anonobj.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ transferinterface.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/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 `/«PKGBUILDDIR»/src/socket' (cd dnaindex ; /usr/bin/make CC="cc" CFLAGS="-c -O3 `pkg-config --cflags glib-2.0`" all ) make[3]: Entering directory `/«PKGBUILDDIR»/src/dnaindex' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_index_interface.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_direct.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_hash.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_count.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_glib_index.c kmer_glib_index.dy: In function 'Wise2_retrieve_by_kmer_KmerGlibIndex': kmer_glib_index.dy:77:48: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] kmer_glib_index.dy: In function 'Wise2_insert_by_kmer_KmerGlibIndex': kmer_glib_index.dy:84:33: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] kmer_glib_index.dy: In function 'Wise2_retrieve_active_kmer_KmerGlibIndex': kmer_glib_index.dy:124:40: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models singleseqspace.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models dnamapping.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models largeseqreader.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_untangler.c kmer_assembly_untangler.dy: In function 'Wise2_old_attempt_forward_untangle_KmerAssembly': kmer_assembly_untangler.dy:568:2: warning: passing argument 4 of 'Wise2_lift_backward_tangled_tail' from incompatible pointer type [enabled by default] kmer_assembly_untangler.h:174:6: note: expected 'int *' but argument is of type 'long int *' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_contig.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_error.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models compressed_protein_index.c compressed_protein_index.dy: In function 'Wise2_add_direct_number_CompressedProteinIndex': compressed_protein_index.dy:223:3: warning: return makes integer from pointer without a cast [enabled by default] make[3]: Leaving directory `/«PKGBUILDDIR»/src/dnaindex' (cd network ; /usr/bin/make CC="cc" CFLAGS="-c -O3 `pkg-config --cflags glib-2.0`" all ) make[3]: Entering directory `/«PKGBUILDDIR»/src/network' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex wise_proteinindex_server.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/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 -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config --libs glib-2.0` -lpthread cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex client_multihspscan.c make[3]: Leaving directory `/«PKGBUILDDIR»/src/network' (cd models ; /usr/bin/make CC="cc" CFLAGS="-c -O3 `pkg-config --cflags glib-2.0`" EXTRALIBS="-lm" HMMER_DEFINE="HMMER_INTERNAL" HMMER_INCLUDE="../HMMer2/" HMMER_LIBS="../HMMer2/" all ) make[3]: Entering directory `/«PKGBUILDDIR»/src/models' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ dnal.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ dnaalign.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ seqaligndisplay.c cc -o dnal dnal.o dnaalign.o seqaligndisplay.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ psw.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ proteinsw.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ sw_wrap.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ abc.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/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 -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/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 -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ dbac.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ dba.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ slimdba.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ bigdba.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ dbadisplay.c cc -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include estwise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparser21.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparameter.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ genestats.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisehsp.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ geneutil.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ geneoutput.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ threestatemodel.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ genefrequency.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ splicesitemodeler.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise4.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise6.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ genestretch6.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise21.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ geneloop21.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ geneloop6.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ genephase6.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ gwlite.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ gwlitemodel.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ gwrap.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ matchsum.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ estwrap.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisemodel.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ phasemodel.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ cdparser.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ genedisplay.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ estwise3.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ estslim3.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ estloop3.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ estfrag3.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ estslimloop.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ gwquickdb.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ threestatedb.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ pfamhmmer1db.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ pwmdna.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../HMMer2/ -DHMMER_INTERNAL -I../base/ -I../dynlibsrc/ wise2xhmmer2.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisemodeldb.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ seqhit.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ standardout.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparser4.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/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 -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/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 -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/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 -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/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 -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ genomewise.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ genomewise9.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ genome_evidence.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ est_evidence.c est_evidence.dy: In function 'Wise2_new_est_GenomeEvidenceUnit': est_evidence.dy:142:16: warning: assignment from incompatible pointer type [enabled by default] cc -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ sywise.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ sywise20.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/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 -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ pseudowise.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/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 -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` promoterwise.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ localdba.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` localcishit.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ localcispara.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ motifmatrix.c motifmatrix.c: In function 'Wise2_MotifConsMatrix_alloc_matrix': motifmatrix.c:408:24: warning: assignment makes integer from pointer without a cast [enabled by default] cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ motifmatrixdp.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ transfactor.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ pairwiseshortdna.c cc -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm `pkg-config --libs glib-2.0` -lpthread cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` hsp2aln_sw.c cc -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm -lpthread -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` ar ru libmodel.a 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 ar: creating libmodel.a make[3]: Leaving directory `/«PKGBUILDDIR»/src/models' /usr/bin/make bin make[3]: Entering directory `/«PKGBUILDDIR»/src' mkdir bin cp models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/promoterwise network/scanwise_server models/scanwise ./bin ./welcome.csh Welcome to Wise2.4 The executable programs are in the ./bin directory You must set your WISECONFIGDIR to the config directory before using the programs ie, type setenv WISECONFIGDIR /«PKGBUILDDIR»/src/../wisecfg/ to try an example, try cd example and then ../bin/genewise road.pep human.genomic to build perl, type make perl and follow the instructions to test the package, type make test make[3]: Leaving directory `/«PKGBUILDDIR»/src' make[2]: Leaving directory `/«PKGBUILDDIR»/src' /usr/bin/make -C debian/manpages.d make[2]: Entering directory `/«PKGBUILDDIR»/debian/manpages.d' docbook-to-man dba.sgml > 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 `/«PKGBUILDDIR»/debian/manpages.d' cat src/models/*.tex src/dynlibsrc/*.tex | perl docs/gettex.pl > docs/temp.tex cat docs/wise2api.tex docs/temp.tex docs/apiend.tex > docs/api.tex sed -i 's/ sw_wrap / sw\\_wrap /' docs/api.tex sed -i 's/label{module_sequence\\_codon}/label{module_sequence_codon}/' docs/api.tex sed -i 's/Wise2::GeneParameter21_wrap/Wise2::GeneParameter21\\_wrap/' docs/api.tex cd docs && pdflatex api.tex This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) entering extended mode (./api.tex LaTeX2e <2009/09/24> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, loaded. (/usr/share/texmf-texlive/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/texmf-texlive/tex/latex/base/tracefnt.sty) (/usr/share/texmf-texlive/tex/latex/base/latexsym.sty)) (/usr/share/texmf-texlive/tex/latex/base/article.cls Document Class: article 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texmf-texlive/tex/latex/base/size10.clo)) No file api.aux. (/usr/share/texmf-texlive/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/texmf-texlive/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, 339414 bytes). Transcript written on api.log. cd docs && pdflatex api.tex This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) entering extended mode (./api.tex LaTeX2e <2009/09/24> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, loaded. (/usr/share/texmf-texlive/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/texmf-texlive/tex/latex/base/tracefnt.sty) (/usr/share/texmf-texlive/tex/latex/base/latexsym.sty)) (/usr/share/texmf-texlive/tex/latex/base/article.cls Document Class: article 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texmf-texlive/tex/latex/base/size10.clo)) (./api.aux) (/usr/share/texmf-texlive/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/texmf-texlive/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, 356015 bytes). Transcript written on api.log. cd docs && pdflatex dynamite.tex This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) entering extended mode (./dynamite.tex LaTeX2e <2009/09/24> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, loaded. (/usr/share/texmf-texlive/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/texmf-texlive/tex/latex/base/tracefnt.sty) (/usr/share/texmf-texlive/tex/latex/base/latexsym.sty)) (/usr/share/texmf-texlive/tex/latex/base/article.cls Document Class: article 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texmf-texlive/tex/latex/base/size10.clo)) No file dynamite.aux. (/usr/share/texmf-texlive/tex/latex/base/ulasy.fd) [1{/var/lib/texmf/fonts/map/ pdftex/updmap/pdftex.map}] No file dynamite.toc. [2] (/usr/share/texmf-texlive/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, 236661 bytes). Transcript written on dynamite.log. cd docs && pdflatex dynamite.tex This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) entering extended mode (./dynamite.tex LaTeX2e <2009/09/24> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, loaded. (/usr/share/texmf-texlive/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/texmf-texlive/tex/latex/base/tracefnt.sty) (/usr/share/texmf-texlive/tex/latex/base/latexsym.sty)) (/usr/share/texmf-texlive/tex/latex/base/article.cls Document Class: article 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texmf-texlive/tex/latex/base/size10.clo)) (./dynamite.aux) (/usr/share/texmf-texlive/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/texmf-texlive/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, 240716 bytes). Transcript written on dynamite.log. cd docs && pdflatex wise2.tex This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) entering extended mode (./wise2.tex LaTeX2e <2009/09/24> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, loaded. (/usr/share/texmf-texlive/tex/latex/base/article.cls Document Class: article 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texmf-texlive/tex/latex/base/size10.clo)) (/usr/share/texmf-texlive/tex/latex/graphics/graphicx.sty (/usr/share/texmf-texlive/tex/latex/graphics/keyval.sty) (/usr/share/texmf-texlive/tex/latex/graphics/graphics.sty (/usr/share/texmf-texlive/tex/latex/graphics/trig.sty) (/etc/texmf/tex/latex/config/graphics.cfg) (/usr/share/texmf-texlive/tex/latex/pdftex-def/pdftex.def))) No file wise2.aux. (/usr/share/texmf-texlive/tex/context/base/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) [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/texmf-texlive/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, 222458 bytes). Transcript written on wise2.log. cd docs && pdflatex wise2.tex This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian) entering extended mode (./wise2.tex LaTeX2e <2009/09/24> Babel and hyphenation patterns for english, usenglishmax, dumylang, noh yphenation, loaded. (/usr/share/texmf-texlive/tex/latex/base/article.cls Document Class: article 2007/10/19 v1.4h Standard LaTeX document class (/usr/share/texmf-texlive/tex/latex/base/size10.clo)) (/usr/share/texmf-texlive/tex/latex/graphics/graphicx.sty (/usr/share/texmf-texlive/tex/latex/graphics/keyval.sty) (/usr/share/texmf-texlive/tex/latex/graphics/graphics.sty (/usr/share/texmf-texlive/tex/latex/graphics/trig.sty) (/etc/texmf/tex/latex/config/graphics.cfg) (/usr/share/texmf-texlive/tex/latex/pdftex-def/pdftex.def))) (./wise2.aux) (/usr/share/texmf-texlive/tex/context/base/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) [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/texmf-texlive/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, 225053 bytes). Transcript written on wise2.log. cd docs && hevea api.tex ./api.tex:18: Warning: File \jobname.htoc not found ./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:18: Warning: File \jobname.htoc not found ./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:18: Warning: File \jobname.htoc not found ./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:18: Warning: File \jobname.htoc not found ./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:21: Warning: File \jobname.htoc not found ./wise2.tex:239: Warning: \hbox ./wise2.tex:241: Warning: \hbox ./wise2.tex:243: Warning: \hbox ./wise2.tex:245: Warning: \hbox ./wise2.tex:247: Warning: \hbox ./wise2.tex:249: Warning: \hbox ./wise2.tex:251: Warning: \hbox ./wise2.tex:253: Warning: \hbox ./wise2.tex:261: Warning: \hbox ./wise2.tex:263: Warning: \hbox ./wise2.tex:265: Warning: \hbox ./wise2.tex:267: Warning: \hbox ./wise2.tex:269: Warning: \hbox ./wise2.tex:271: Warning: \hbox ./wise2.tex:273: Warning: \hbox ./wise2.tex:275: Warning: \hbox ./wise2.tex:706: Warning: Undefined label: 'Figure:genewise21' ./wise2.tex:710: Warning: Command not found: \leavevmode ./wise2.tex:902: Warning: Command not found: \leavevmode cd docs && hevea wise2.tex ./wise2.tex:21: Warning: File \jobname.htoc not found ./wise2.tex:239: Warning: \hbox ./wise2.tex:241: Warning: \hbox ./wise2.tex:243: Warning: \hbox ./wise2.tex:245: Warning: \hbox ./wise2.tex:247: Warning: \hbox ./wise2.tex:249: Warning: \hbox ./wise2.tex:251: Warning: \hbox ./wise2.tex:253: Warning: \hbox ./wise2.tex:261: Warning: \hbox ./wise2.tex:263: Warning: \hbox ./wise2.tex:265: Warning: \hbox ./wise2.tex:267: Warning: \hbox ./wise2.tex:269: Warning: \hbox ./wise2.tex:271: Warning: \hbox ./wise2.tex:273: Warning: \hbox ./wise2.tex:275: Warning: \hbox ./wise2.tex:706: Warning: Undefined label: 'Figure:genewise21' ./wise2.tex:710: Warning: Command not found: \leavevmode ./wise2.tex:902: Warning: Command not found: \leavevmode mkdir -p docs/api mkdir -p docs/dynamite mkdir -p docs/wise2 mv docs/api.html docs/api mv docs/dynamite.html docs/dynamite mv docs/wise2.html docs/wise2 touch override_dh_auto_build make[1]: Leaving directory `/«PKGBUILDDIR»' dh_auto_test -a fakeroot debian/rules binary-arch dh binary-arch --with quilt dh_testroot -a dh_prep -a rm -f debian/wise.substvars rm -f debian/wise.*.debhelper rm -rf debian/wise/ dh_installdirs -a install -d debian/wise install -d debian/wise/usr/bin dh_auto_install -a debian/rules override_dh_install make[1]: Entering directory `/«PKGBUILDDIR»' install -m 755 src/bin/* debian/wise/usr/bin install -m 755 src/models/genomewise debian/wise/usr/bin make[1]: Leaving directory `/«PKGBUILDDIR»' dh_installdocs -a install -g 0 -o 0 -d debian/wise/usr/share/doc/wise cp -a README debian/wise/usr/share/doc/wise chown -R 0:0 debian/wise/usr/share/doc chmod -R go=rX debian/wise/usr/share/doc chmod -R u\+rw debian/wise/usr/share/doc install -g 0 -o 0 -m 644 -p debian/README.Debian debian/wise/usr/share/doc/wise/README.Debian install -g 0 -o 0 -m 644 -p debian/copyright debian/wise/usr/share/doc/wise/copyright dh_installchangelogs -a install -o 0 -g 0 -p -m644 debian/changelog debian/wise/usr/share/doc/wise/changelog.Debian dh_installexamples -a dh_installman -a 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 ./genewise\.1 > genewise\.1\.new chmod 644 genewise.1.new mv -f genewise.1.new genewise.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 ./pswdb\.1 > pswdb\.1\.new chmod 644 pswdb.1.new mv -f pswdb.1.new pswdb.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 ./genewisedb\.1 > genewisedb\.1\.new chmod 644 genewisedb.1.new mv -f genewisedb.1.new genewisedb.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 ./genomewise\.1 > genomewise\.1\.new chmod 644 genomewise.1.new mv -f genomewise.1.new genomewise.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 ./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 ./estwise\.1 > estwise\.1\.new chmod 644 estwise.1.new mv -f estwise.1.new estwise.1 man --recode UTF-8 ./estwisedb\.1 > estwisedb\.1\.new chmod 644 estwisedb.1.new mv -f estwisedb.1.new estwisedb.1 dh_installcatalogs -a dh_installcron -a dh_installdebconf -a install -o 0 -g 0 -d debian/wise/DEBIAN dh_installemacsen -a dh_installifupdown -a dh_installinfo -a dh_installinit -a dh_installmenu -a dh_installmime -a dh_installmodules -a dh_installlogcheck -a dh_installlogrotate -a dh_installpam -a dh_installppp -a dh_installudev -a dh_installwm -a dh_installxfonts -a dh_installgsettings -a dh_bugfiles -a dh_ucf -a dh_lintian -a dh_gconf -a dh_icons -a dh_perl -a dh_usrlocal -a dh_link -a dh_compress -a cd debian/wise chmod a-x usr/share/man/man1/genewise.1 usr/share/man/man1/psw.1 usr/share/man/man1/pswdb.1 usr/share/man/man1/dba.1 usr/share/man/man1/genewisedb.1 usr/share/man/man1/scanwise_server.1 usr/share/man/man1/genomewise.1 usr/share/man/man1/promoterwise.1 usr/share/man/man1/dnal.1 usr/share/man/man1/scanwise.1 usr/share/man/man1/estwise.1 usr/share/man/man1/estwisedb.1 usr/share/doc/wise/changelog.Debian gzip -9nf usr/share/man/man1/genewise.1 usr/share/man/man1/psw.1 usr/share/man/man1/pswdb.1 usr/share/man/man1/dba.1 usr/share/man/man1/genewisedb.1 usr/share/man/man1/scanwise_server.1 usr/share/man/man1/genomewise.1 usr/share/man/man1/promoterwise.1 usr/share/man/man1/dnal.1 usr/share/man/man1/scanwise.1 usr/share/man/man1/estwise.1 usr/share/man/man1/estwisedb.1 usr/share/doc/wise/changelog.Debian cd '/«PKGBUILDDIR»' dh_fixperms -a find debian/wise -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0 find debian/wise ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/wise/usr/share/doc -type f ! -regex 'debian/wise/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644 find debian/wise/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755 find debian/wise/usr/share/man debian/wise/usr/man/ debian/wise/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/wise -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644 find debian/wise/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/wise/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644 find debian/wise -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644 find debian/wise/usr/lib/perl5 debian/wise/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X find debian/wise/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x find debian/wise/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w dh_strip -a strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/psw strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/estwisedb strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/estwise strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genewisedb strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/scanwise strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genomewise strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/dnal strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/promoterwise strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/dba strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/scanwise_server strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genewise strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/pswdb dh_makeshlibs -a rm -f debian/wise/DEBIAN/shlibs dh_shlibdeps -a dpkg-shlibdeps -Tdebian/wise.substvars debian/wise/usr/bin/psw debian/wise/usr/bin/estwisedb debian/wise/usr/bin/estwise debian/wise/usr/bin/genewisedb debian/wise/usr/bin/scanwise debian/wise/usr/bin/genomewise debian/wise/usr/bin/dnal debian/wise/usr/bin/promoterwise debian/wise/usr/bin/dba debian/wise/usr/bin/scanwise_server debian/wise/usr/bin/genewise debian/wise/usr/bin/pswdb dh_installdeb -a dh_gencontrol -a echo misc:Depends= >> debian/wise.substvars dpkg-gencontrol -pwise -ldebian/changelog -Tdebian/wise.substvars -Pdebian/wise chmod 644 debian/wise/DEBIAN/control chown 0:0 debian/wise/DEBIAN/control dh_md5sums -a (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 debian/rules override_dh_builddeb make[1]: Entering directory `/«PKGBUILDDIR»' dh_builddeb -- -Z xz dpkg-deb -Z xz --build debian/wise .. dpkg-deb: building package `wise' in `../wise_2.4.1-10_armhf.deb'. make[1]: Leaving directory `/«PKGBUILDDIR»' dpkg-genchanges -B -mbuildd >../wise_2.4.1-10_armhf.changes dpkg-genchanges: arch-specific upload - not including arch-independent packages dpkg-genchanges: binary-only upload - not including any source code dpkg-source --after-build wise-2.4.1 dpkg-buildpackage: binary only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20120505-0019 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ wise_2.4.1-10_armhf.changes: ──────────────────────────── Format: 1.8 Date: Fri, 30 Mar 2012 19:25:53 +0900 Source: wise Binary: wise wise-doc Architecture: armhf Version: 2.4.1-10 Distribution: testing Urgency: low Maintainer: buildd Changed-By: Charles Plessy Description: wise - comparison of biopolymers, commonly DNA and protein sequences wise-doc - documentation for the wise package Closes: 666319 Changes: wise (2.4.1-10) unstable; urgency=low . * Convert debian/rules to dh, Closes: #666319, as it restores build flags. * Verbose debhelper in debian/rules. * Normalised and upgraded debian/copyright file with ‘cme fix’. * Pre-Depends on dpkg (>= 1.15.6~) (debian/control). * Conforms to Debian policy 3.9.3 (debian/control, no other changes needed). * Convert debian/rules to dh, Closes: #666319, as it restores build flags. * Documented metadata in debian/upstream. Checksums-Sha1: dc6222ef4e3cd07d8f2e2e9cef1dcd98cdcdfa22 853446 wise_2.4.1-10_armhf.deb Checksums-Sha256: 6b67a222456220162933b427c9f74bc53e918b53bad670deae04a73957ec3b56 853446 wise_2.4.1-10_armhf.deb Files: 20cbbb7e00d54e98d25a019ac876babf 853446 science optional wise_2.4.1-10_armhf.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ wise_2.4.1-10_armhf.deb ─────────────────────── new debian package, version 2.0. size 853446 bytes: control archive= 1926 bytes. 1733 bytes, 34 lines control 1675 bytes, 28 lines md5sums Package: wise Version: 2.4.1-10 Architecture: armhf Maintainer: Debian Med Packaging Team Installed-Size: 9846 Pre-Depends: dpkg (>= 1.15.6~) Depends: libc6 (>= 2.13-28), libglib2.0-0 (>= 2.12.0) Suggests: wise-doc (= 2.4.1-10) Section: science Priority: optional Homepage: http://www.ebi.ac.uk/~birney/wise2/ Description: comparison of biopolymers, commonly DNA and protein sequences Wise2 is a package focused on comparisons of biopolymers, commonly DNA and protein sequences. There are many other packages which do this, probably the best known being BLAST package (from NCBI) and the Fasta package (from Bill Pearson). There are other packages, such as the HMMER package (Sean Eddy) or SAM package (UC Santa Cruz) focused on hidden Markov models (HMMs) of biopolymers. . Wise2's particular forte is the comparison of DNA sequence at the level of its protein translation. This comparison allows the simultaneous prediction of say gene structure with homology based alignment. . Wise2 also contains other algorithms, such as the venerable Smith-Waterman algorithm, or more modern ones such as Stephen Altschul's generalised gap penalties, or even experimental ones developed in house, such as dba. The development of these algorithms is due to the ease of developing such algorithms in the environment used by Wise2. . Wise2 has also been written with an eye for reuse and maintainability. Although it is a pure C package you can access its functionality directly in Perl. Parts of the package (or the entire package) can be used by other C or C++ programs without namespace clashes as all externally linked variables have the unique identifier Wise2 prepended. drwxr-xr-x root/root 0 2012-05-05 00:17 ./ drwxr-xr-x root/root 0 2012-05-05 00:17 ./usr/ drwxr-xr-x root/root 0 2012-05-05 00:17 ./usr/share/ drwxr-xr-x root/root 0 2012-05-05 00:17 ./usr/share/doc/ drwxr-xr-x root/root 0 2012-05-05 00:18 ./usr/share/doc/wise/ -rw-r--r-- root/root 1973 2007-07-01 13:46 ./usr/share/doc/wise/README -rw-r--r-- root/root 1902 2012-05-04 23:53 ./usr/share/doc/wise/changelog.Debian.gz -rw-r--r-- root/root 4219 2012-05-04 23:53 ./usr/share/doc/wise/copyright -rw-r--r-- root/root 320 2012-05-04 23:53 ./usr/share/doc/wise/README.Debian drwxr-xr-x root/root 0 2012-05-05 00:17 ./usr/share/man/ drwxr-xr-x root/root 0 2012-05-05 00:18 ./usr/share/man/man1/ -rw-r--r-- root/root 618 2012-05-05 00:17 ./usr/share/man/man1/estwise.1.gz -rw-r--r-- root/root 627 2012-05-05 00:17 ./usr/share/man/man1/genomewise.1.gz -rw-r--r-- root/root 624 2012-05-05 00:17 ./usr/share/man/man1/scanwise.1.gz -rw-r--r-- root/root 615 2012-05-05 00:17 ./usr/share/man/man1/promoterwise.1.gz -rw-r--r-- root/root 708 2012-05-05 00:17 ./usr/share/man/man1/psw.1.gz -rw-r--r-- root/root 579 2012-05-05 00:17 ./usr/share/man/man1/dnal.1.gz -rw-r--r-- root/root 619 2012-05-05 00:17 ./usr/share/man/man1/genewisedb.1.gz -rw-r--r-- root/root 617 2012-05-05 00:17 ./usr/share/man/man1/estwisedb.1.gz -rw-r--r-- root/root 607 2012-05-05 00:17 ./usr/share/man/man1/scanwise_server.1.gz -rw-r--r-- root/root 608 2012-05-05 00:17 ./usr/share/man/man1/pswdb.1.gz -rw-r--r-- root/root 871 2012-05-05 00:17 ./usr/share/man/man1/dba.1.gz -rw-r--r-- root/root 617 2012-05-05 00:17 ./usr/share/man/man1/genewise.1.gz drwxr-xr-x root/root 0 2012-05-05 00:18 ./usr/bin/ -rwxr-xr-x root/root 272476 2012-05-05 00:18 ./usr/bin/psw -rwxr-xr-x root/root 1952840 2012-05-05 00:18 ./usr/bin/estwisedb -rwxr-xr-x root/root 1948656 2012-05-05 00:18 ./usr/bin/estwise -rwxr-xr-x root/root 1956984 2012-05-05 00:18 ./usr/bin/genewisedb -rwxr-xr-x root/root 391868 2012-05-05 00:18 ./usr/bin/scanwise -rwxr-xr-x root/root 321824 2012-05-05 00:18 ./usr/bin/genomewise -rwxr-xr-x root/root 182200 2012-05-05 00:18 ./usr/bin/dnal -rwxr-xr-x root/root 336008 2012-05-05 00:18 ./usr/bin/promoterwise -rwxr-xr-x root/root 281768 2012-05-05 00:18 ./usr/bin/dba -rwxr-xr-x root/root 154852 2012-05-05 00:18 ./usr/bin/scanwise_server -rwxr-xr-x root/root 1952816 2012-05-05 00:18 ./usr/bin/genewise -rwxr-xr-x root/root 276760 2012-05-05 00:18 ./usr/bin/pswdb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Purging /«BUILDDIR» Reading package lists... Building dependency tree... Reading state information... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bsdmainutils* debhelper* diffstat* docbook* docbook-to-man* ed* file* fontconfig-config* gettext* gettext-base* ghostscript* groff-base* gs-cjk-resource* gsfonts* hevea* html2text* intltool-debian* libavahi-client3* libavahi-common-data* libavahi-common3* libcroco3* libcups2* libcupsimage2* libdb4.8* libdbus-1-3* libelf1* libexpat1* libffi5* libfontconfig1* libfreetype6* libgcrypt11* libglib2.0-0* libglib2.0-bin* libglib2.0-data* libglib2.0-dev* libgnutls26* libgpg-error0* libgs9* libgs9-common* libgssapi-krb5-2* libice6* libidn11* libijs-0.35* libjasper1* libjbig0* libjbig2dec0* libjpeg8* libk5crypto3* libkeyutils1* libkpathsea5* libkrb5-3* libkrb5support0* liblcms1* liblcms2-2* libmagic1* libnetpbm10* libopenjpeg2* libp11-kit0* libpaper-utils* libpaper1* libpcre3* libpcre3-dev* libpcrecpp0* libpipeline1* libpng12-0* libpoppler13* libpopt0* libsm6* libsp1c2* libsqlite3-0* libssl1.0.0* libtasn1-3* libtiff4* libunistring0* libx11-6* libx11-data* libxau6* libxaw7* libxcb1* libxdmcp6* libxext6* libxml2* libxmu6* libxpm4* libxt6* luatex* man-db* mime-support* netpbm* ocaml-base-nox* pkg-config* po-debconf* python* python-minimal* python2.7* python2.7-minimal* quilt* sbuild-build-depends-core-dummy* sbuild-build-depends-wise-dummy* sgml-base* sgml-data* sp* tex-common* texlive-base* texlive-binaries* texlive-common* texlive-doc-base* texlive-extra-utils* texlive-latex-base* ttf-dejavu-core* x11-common* xml-core* zlib1g-dev* 0 upgraded, 0 newly installed, 113 to remove and 0 not upgraded. After this operation, 183 MB disk space will be freed. (Reading database ... 20115 files and directories currently installed.) Removing sbuild-build-depends-wise-dummy ... Removing quilt ... Purging configuration files for quilt ... Removing debhelper ... Removing man-db ... Purging configuration files for man-db ... Removing bsdmainutils ... Purging configuration files for bsdmainutils ... Removing diffstat ... Removing docbook-to-man ... Removing docbook ... Purging configuration files for docbook ... Removing texlive-latex-base ... Purging configuration files for texlive-latex-base ... Removing texlive-extra-utils ... Purging configuration files for texlive-extra-utils ... Removing hevea ... Purging configuration files for hevea ... Removing texlive-base ... Purging configuration files for texlive-base ... Removing texlive-binaries ... Removing ed ... Removing file ... Removing luatex ... Removing libpoppler13 ... Purging configuration files for libpoppler13 ... 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Purging configuration files for gsfonts ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Architecture: armhf Build-Space: 71560 Build-Time: 1518 Distribution: testing Install-Time: 275 Job: wise_2.4.1-10 Package: wise Package-Time: 1811 Source-Version: 2.4.1-10 Space: 71560 Status: successful Version: 2.4.1-10 ──────────────────────────────────────────────────────────────────────────────── Finished at 20120505-0019 Build needed 00:30:11, 71560k disc space