sbuild (Debian sbuild) 0.85.0 (04 January 2023) on debian-ci-siliconvalley +==============================================================================+ | wise 2.4.1-23 (arm64) Sun, 07 Jan 2024 00:54:16 +0000 | +==============================================================================+ Package: wise Version: 2.4.1-23 Source Version: 2.4.1-23 Distribution: unstable Machine Architecture: amd64 Host Architecture: arm64 Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-0e395cfd-3c89-452e-9bc4-c899112f44cd' with '<>' I: NOTICE: Log filtering will replace 'build/wise-Ua1ga6/resolver-jCW8xN' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://localhost:3142/debian sid InRelease Get:2 http://localhost:3142/debian sid/main arm64 Packages [9521 kB] Fetched 9521 kB in 1s (8625 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'wise' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/wise.git Please use: git clone https://salsa.debian.org/med-team/wise.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 3440 kB of source archives. Get:1 http://localhost:3142/debian sid/main wise 2.4.1-23 (dsc) [2179 B] Get:2 http://localhost:3142/debian sid/main wise 2.4.1-23 (tar) [3410 kB] Get:3 http://localhost:3142/debian sid/main wise 2.4.1-23 (diff) [27.2 kB] Fetched 3440 kB in 1s (2799 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/wise-Ua1ga6/wise-2.4.1' with '<>' I: NOTICE: Log filtering will replace 'build/wise-Ua1ga6' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), texlive-latex-base, texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-arm64:amd64, libc-dev:arm64, libstdc++-dev:arm64 Filtered Build-Depends: debhelper-compat (= 12), texlive-latex-base, texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-arm64:amd64, libc-dev:arm64, libstdc++-dev:arm64 dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [609 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [794 B] Get:5 copy:/<>/apt_archive ./ Packages [837 B] Fetched 2240 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... Execute external solver... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-aarch64-linux-gnu bsdextrautils cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu cross-config crossbuild-essential-arm64 debhelper dh-autoreconf dh-strip-nondeterminism docbook docbook-to-man dpkg-cross dwz file fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lmodern fonts-urw-base35 g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-11-base:arm64 gcc-13-aarch64-linux-gnu gcc-13-aarch64-linux-gnu-base gcc-13-base:arm64 gcc-13-cross-base gcc-aarch64-linux-gnu gettext gettext-base ghostscript groff-base hevea hicolor-icon-theme imagemagick imagemagick-6-common imagemagick-6.q16 intltool-debian libarchive-zip-perl libasan6:arm64 libasan8-arm64-cross libatomic1:arm64 libatomic1-arm64-cross libavahi-client3 libavahi-common-data libavahi-common3 libblkid-dev:arm64 libblkid1:arm64 libbrotli1 libbsd0 libc6:arm64 libc6-arm64-cross libc6-dev:arm64 libc6-dev-arm64-cross libcairo2 libcom-err2:arm64 libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:arm64 libcrypt1:arm64 libcups2 libdatrie1 libdav1d7 libdbus-1-3 libde265-0 libdebhelper-perl libdebian-dpkgcross-perl libdeflate0 libelf1 libexpat1 libffi-dev:arm64 libffi8:arm64 libfftw3-double3 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libfontconfig1 libfontenc1 libfreetype6 libgcc-11-dev:arm64 libgcc-13-dev-arm64-cross libgcc-s1:arm64 libgcc-s1-arm64-cross libglib2.0-0 libglib2.0-0:arm64 libglib2.0-bin libglib2.0-data libglib2.0-dev:arm64 libglib2.0-dev-bin libgomp1:arm64 libgomp1-arm64-cross libgraphite2-3 libgs-common libgs10 libgs10-common libgssapi-krb5-2:arm64 libharfbuzz0b libheif-plugin-dav1d libheif-plugin-libde265 libheif1 libhwasan0:arm64 libhwasan0-arm64-cross libice6 libicu72 libidn12 libijs-0.35 libio-string-perl libitm1:arm64 libitm1-arm64-cross libjbig0 libjbig2dec0 libjpeg62-turbo libjs-jquery libk5crypto3:arm64 libkeyutils1:arm64 libkpathsea6 libkrb5-3:arm64 libkrb5support0:arm64 liblcms2-2 liblerc4 liblocale-gettext-perl liblqr-1-0 liblsan0:arm64 liblsan0-arm64-cross libltdl7 libmagic-mgc libmagic1 libmagickcore-6.q16-7 libmagickwand-6.q16-7 libmime-charset-perl libmount-dev:arm64 libmount1:arm64 libncursesw6 libnetpbm11 libnsl-dev:arm64 libnsl2:arm64 libopenjp2-7 libosp5 libpaper-utils libpaper1 libpcre2-16-0:arm64 libpcre2-32-0:arm64 libpcre2-8-0:arm64 libpcre2-dev:arm64 libpcre2-posix3:arm64 libpipeline1 libpixman-1-0 libpkgconf3 libpng16-16 libpotrace0 libptexenc1 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libraw23 libreadline8 libselinux1:arm64 libselinux1-dev:arm64 libsepol-dev:arm64 libsepol2:arm64 libsharpyuv0 libsm6 libsombok3 libsqlite3-0 libssl3:arm64 libstdc++-11-dev:arm64 libstdc++-13-dev-arm64-cross libstdc++6:arm64 libstdc++6-arm64-cross libsub-override-perl libsynctex2 libteckit0 libtexlua53-5 libthai-data libthai0 libtiff6 libtirpc-dev:arm64 libtirpc3:arm64 libtool libtsan0:arm64 libtsan2-arm64-cross libubsan1:arm64 libubsan1-arm64-cross libuchardet0 libunicode-linebreak-perl libuuid1:arm64 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libxmu6 libxpm4 libxrender1 libxt6 libyaml-perl libyaml-tiny-perl libzzip-0-13 linux-libc-dev-arm64-cross lmodern m4 man-db media-types netbase netpbm opensp pkg-config:arm64 pkgconf:arm64 pkgconf-bin po-debconf poppler-data python3 python3-distutils python3-lib2to3 python3-minimal python3.11 python3.11-minimal readline-common sensible-utils sgml-base sgml-data t1utils tex-common texlive-base texlive-binaries texlive-extra-utils texlive-latex-base texlive-luatex texlive-plain-generic ucf uuid-dev:arm64 x11-common xdg-utils xfonts-encodings xfonts-utils xml-core zlib1g:arm64 zlib1g-dev:arm64 Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-13-locales cpp-13-doc cpp-doc dh-make docbook-defguide docbook-dsssl docbook-xml psgml binutils-multiarch fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre gcc-13-doc manpages-dev flex bison gdb-aarch64-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff hevea-doc texlive-latex-extra imagemagick-6-doc autotrace cups-bsd | lpr | lprng curl enscript ffmpeg gimp gnuplot grads graphviz hp2xx html2ps libwmf-bin mplayer povray radiance sane-utils transfig libraw-bin glibc-doc:arm64 libc-l10n:arm64 locales:arm64 libnss-nis:arm64 libnss-nisplus:arm64 manpages-dev:arm64 cups-common libfftw3-bin libfftw3-dev low-memory-monitor low-memory-monitor:arm64 libgirepository1.0-dev:arm64 libglib2.0-doc:arm64 libgdk-pixbuf2.0-bin libxml2-utils krb5-doc:arm64 krb5-user:arm64 libheif-plugin-ffmpegdec libheif-plugin-jpegdec libheif-plugin-jpegenc libheif-plugin-j2kdec libheif-plugin-j2kenc libheif-plugin-rav1e libheif-plugin-svtenc liblcms2-utils libmagickcore-6.q16-7-extra libencode-eucjpascii-perl libencode-hanextra-perl libpod2-base-perl cryptsetup-bin:arm64 libstdc++-11-doc:arm64 libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser doc-base libmail-box-perl poppler-utils fonts-japanese-mincho | fonts-ipafont-mincho fonts-japanese-gothic | fonts-ipafont-gothic fonts-arphic-ukai fonts-arphic-uming fonts-nanum python3-doc python3-tk python3-venv python3.11-venv python3.11-doc binfmt-support readline-doc sgml-base-doc perlsgml w3-recs perl-tk xpdf | pdf-viewer xzdec texlive-binaries-sse2 hintview chktex default-jre-headless dvidvi dvipng fragmaster lacheck latexdiff latexmk purifyeps xindy texlive-latex-base-doc wp2latex Recommended packages: curl | wget | lynx libmagickcore-6.q16-7-extra libidn2-0:arm64 dbus libarchive-cpio-perl shared-mime-info xdg-user-dirs shared-mime-info:arm64 xdg-user-dirs:arm64 fonts-droid-fallback libheif-plugin-aomenc libheif-plugin-x265 javascript-common krb5-locales:arm64 libgpm2 libltdl-dev uuid-runtime:arm64 libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl ca-certificates dvisvgm liblog-log4perl-perl ruby texlive-latex-recommended libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-aarch64-linux-gnu bsdextrautils cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu cross-config crossbuild-essential-arm64 debhelper dh-autoreconf dh-strip-nondeterminism docbook docbook-to-man dpkg-cross dwz file fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lmodern fonts-urw-base35 g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-11-base:arm64 gcc-13-aarch64-linux-gnu gcc-13-aarch64-linux-gnu-base gcc-13-base:arm64 gcc-13-cross-base gcc-aarch64-linux-gnu gettext gettext-base ghostscript groff-base hevea hicolor-icon-theme imagemagick imagemagick-6-common imagemagick-6.q16 intltool-debian libarchive-zip-perl libasan6:arm64 libasan8-arm64-cross libatomic1:arm64 libatomic1-arm64-cross libavahi-client3 libavahi-common-data libavahi-common3 libblkid-dev:arm64 libblkid1:arm64 libbrotli1 libbsd0 libc6:arm64 libc6-arm64-cross libc6-dev:arm64 libc6-dev-arm64-cross libcairo2 libcom-err2:arm64 libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:arm64 libcrypt1:arm64 libcups2 libdatrie1 libdav1d7 libdbus-1-3 libde265-0 libdebhelper-perl libdebian-dpkgcross-perl libdeflate0 libelf1 libexpat1 libffi-dev:arm64 libffi8:arm64 libfftw3-double3 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libfontconfig1 libfontenc1 libfreetype6 libgcc-11-dev:arm64 libgcc-13-dev-arm64-cross libgcc-s1:arm64 libgcc-s1-arm64-cross libglib2.0-0 libglib2.0-0:arm64 libglib2.0-bin libglib2.0-data libglib2.0-dev:arm64 libglib2.0-dev-bin libgomp1:arm64 libgomp1-arm64-cross libgraphite2-3 libgs-common libgs10 libgs10-common libgssapi-krb5-2:arm64 libharfbuzz0b libheif-plugin-dav1d libheif-plugin-libde265 libheif1 libhwasan0:arm64 libhwasan0-arm64-cross libice6 libicu72 libidn12 libijs-0.35 libio-string-perl libitm1:arm64 libitm1-arm64-cross libjbig0 libjbig2dec0 libjpeg62-turbo libjs-jquery libk5crypto3:arm64 libkeyutils1:arm64 libkpathsea6 libkrb5-3:arm64 libkrb5support0:arm64 liblcms2-2 liblerc4 liblocale-gettext-perl liblqr-1-0 liblsan0:arm64 liblsan0-arm64-cross libltdl7 libmagic-mgc libmagic1 libmagickcore-6.q16-7 libmagickwand-6.q16-7 libmime-charset-perl libmount-dev:arm64 libmount1:arm64 libncursesw6 libnetpbm11 libnsl-dev:arm64 libnsl2:arm64 libopenjp2-7 libosp5 libpaper-utils libpaper1 libpcre2-16-0:arm64 libpcre2-32-0:arm64 libpcre2-8-0:arm64 libpcre2-dev:arm64 libpcre2-posix3:arm64 libpipeline1 libpixman-1-0 libpkgconf3 libpng16-16 libpotrace0 libptexenc1 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libraw23 libreadline8 libselinux1:arm64 libselinux1-dev:arm64 libsepol-dev:arm64 libsepol2:arm64 libsharpyuv0 libsm6 libsombok3 libsqlite3-0 libssl3:arm64 libstdc++-11-dev:arm64 libstdc++-13-dev-arm64-cross libstdc++6:arm64 libstdc++6-arm64-cross libsub-override-perl libsynctex2 libteckit0 libtexlua53-5 libthai-data libthai0 libtiff6 libtirpc-dev:arm64 libtirpc3:arm64 libtool libtsan0:arm64 libtsan2-arm64-cross libubsan1:arm64 libubsan1-arm64-cross libuchardet0 libunicode-linebreak-perl libuuid1:arm64 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libxmu6 libxpm4 libxrender1 libxt6 libyaml-perl libyaml-tiny-perl libzzip-0-13 linux-libc-dev-arm64-cross lmodern m4 man-db media-types netbase netpbm opensp pkg-config:arm64 pkgconf:arm64 pkgconf-bin po-debconf poppler-data python3 python3-distutils python3-lib2to3 python3-minimal python3.11 python3.11-minimal readline-common sbuild-build-depends-main-dummy:arm64 sensible-utils sgml-base sgml-data t1utils tex-common texlive-base texlive-binaries texlive-extra-utils texlive-latex-base texlive-luatex texlive-plain-generic ucf uuid-dev:arm64 x11-common xdg-utils xfonts-encodings xfonts-utils xml-core zlib1g:arm64 zlib1g-dev:arm64 0 upgraded, 256 newly installed, 0 to remove and 0 not upgraded. Need to get 319 MB of archives. After this operation, 945 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [968 B] Get:2 http://localhost:3142/debian sid/main amd64 liblocale-gettext-perl amd64 1.07-6 [15.3 kB] Get:3 http://localhost:3142/debian sid/main amd64 libfftw3-double3 amd64 3.3.10-1 [776 kB] Get:4 http://localhost:3142/debian sid/main amd64 libexpat1 amd64 2.5.0-2+b2 [99.4 kB] Get:5 http://localhost:3142/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get:6 http://localhost:3142/debian sid/main amd64 libpng16-16 amd64 1.6.40-3 [276 kB] Get:7 http://localhost:3142/debian sid/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b1 [439 kB] Get:8 http://localhost:3142/debian sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:9 http://localhost:3142/debian sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:10 http://localhost:3142/debian sid/main amd64 libfontenc1 amd64 1:1.1.4-1+b2 [23.3 kB] Get:11 http://localhost:3142/debian sid/main amd64 x11-common all 1:7.7+23 [252 kB] Get:12 http://localhost:3142/debian sid/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get:13 http://localhost:3142/debian sid/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB] Get:14 http://localhost:3142/debian sid/main amd64 fonts-urw-base35 all 20200910-7 [10.8 MB] Get:15 http://localhost:3142/debian sid/main amd64 fontconfig-config amd64 2.14.2-6+b1 [316 kB] Get:16 http://localhost:3142/debian sid/main amd64 libfontconfig1 amd64 2.14.2-6+b1 [388 kB] Get:17 http://localhost:3142/debian sid/main amd64 libsharpyuv0 amd64 1.3.2-0.3 [107 kB] Get:18 http://localhost:3142/debian sid/main amd64 libdav1d7 amd64 1.3.0-2+b1 [543 kB] Get:19 http://localhost:3142/debian sid/main amd64 libheif-plugin-dav1d amd64 1.17.6-1 [9592 B] Get:20 http://localhost:3142/debian sid/main amd64 libde265-0 amd64 1.0.15-1 [187 kB] Get:21 http://localhost:3142/debian sid/main amd64 libheif-plugin-libde265 amd64 1.17.6-1 [12.9 kB] Get:22 http://localhost:3142/debian sid/main amd64 libheif1 amd64 1.17.6-1 [284 kB] Get:23 http://localhost:3142/debian sid/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get:24 http://localhost:3142/debian sid/main amd64 libjpeg62-turbo amd64 1:2.1.5-2+b2 [167 kB] Get:25 http://localhost:3142/debian sid/main amd64 liblcms2-2 amd64 2.14-2 [154 kB] Get:26 http://localhost:3142/debian sid/main amd64 libglib2.0-0 amd64 2.78.3-1 [1452 kB] Get:27 http://localhost:3142/debian sid/main amd64 liblqr-1-0 amd64 0.4.2-2.1 [29.1 kB] Get:28 http://localhost:3142/debian sid/main amd64 libltdl7 amd64 2.4.7-7 [393 kB] Get:29 http://localhost:3142/debian sid/main amd64 libopenjp2-7 amd64 2.5.0-2+b2 [190 kB] Get:30 http://localhost:3142/debian sid/main amd64 libraw23 amd64 0.21.1-7 [386 kB] Get:31 http://localhost:3142/debian sid/main amd64 libdeflate0 amd64 1.18-1 [40.9 kB] Get:32 http://localhost:3142/debian sid/main amd64 liblerc4 amd64 4.0.0+ds-4 [170 kB] Get:33 http://localhost:3142/debian sid/main amd64 libwebp7 amd64 1.3.2-0.3 [308 kB] Get:34 http://localhost:3142/debian sid/main amd64 libtiff6 amd64 4.5.1+git230720-3 [323 kB] Get:35 http://localhost:3142/debian sid/main amd64 libwebpdemux2 amd64 1.3.2-0.3 [107 kB] Get:36 http://localhost:3142/debian sid/main amd64 libwebpmux3 amd64 1.3.2-0.3 [120 kB] Get:37 http://localhost:3142/debian sid/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:38 http://localhost:3142/debian sid/main amd64 libbsd0 amd64 0.11.7-4 [115 kB] Get:39 http://localhost:3142/debian sid/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:40 http://localhost:3142/debian sid/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get:41 http://localhost:3142/debian sid/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:42 http://localhost:3142/debian sid/main amd64 libx11-6 amd64 2:1.8.7-1 [802 kB] Get:43 http://localhost:3142/debian sid/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:44 http://localhost:3142/debian sid/main amd64 libicu72 amd64 72.1-4 [9396 kB] Get:45 http://localhost:3142/debian sid/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b2 [692 kB] Get:46 http://localhost:3142/debian sid/main amd64 imagemagick-6-common all 8:6.9.12.98+dfsg1-5 [66.9 kB] Get:47 http://localhost:3142/debian sid/main amd64 libmagickcore-6.q16-7 amd64 8:6.9.12.98+dfsg1-5 [1698 kB] Get:48 http://localhost:3142/debian sid/main amd64 libmagickwand-6.q16-7 amd64 8:6.9.12.98+dfsg1-5 [310 kB] Get:49 http://localhost:3142/debian sid/main amd64 poppler-data all 0.4.12-1 [1601 kB] Get:50 http://localhost:3142/debian sid/main amd64 libpython3.11-minimal amd64 3.11.7-2 [816 kB] Get:51 http://localhost:3142/debian sid/main amd64 python3.11-minimal amd64 3.11.7-2 [2035 kB] Get:52 http://localhost:3142/debian sid/main amd64 python3-minimal amd64 3.11.6-1 [26.2 kB] Get:53 http://localhost:3142/debian sid/main amd64 media-types all 10.1.0 [26.9 kB] Get:54 http://localhost:3142/debian sid/main amd64 netbase all 6.4 [12.8 kB] Get:55 http://localhost:3142/debian sid/main amd64 libncursesw6 amd64 6.4+20231209-1 [135 kB] Get:56 http://localhost:3142/debian sid/main amd64 readline-common all 8.2-3 [69.1 kB] Get:57 http://localhost:3142/debian sid/main amd64 libreadline8 amd64 8.2-3 [167 kB] Get:58 http://localhost:3142/debian sid/main amd64 libsqlite3-0 amd64 3.44.2-1 [882 kB] Get:59 http://localhost:3142/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.7-2 [1822 kB] Get:60 http://localhost:3142/debian sid/main amd64 python3.11 amd64 3.11.7-2 [590 kB] Get:61 http://localhost:3142/debian sid/main amd64 libpython3-stdlib amd64 3.11.6-1 [9224 B] Get:62 http://localhost:3142/debian sid/main amd64 python3 amd64 3.11.6-1 [26.2 kB] Get:63 http://localhost:3142/debian sid/main amd64 sgml-base all 1.31 [15.4 kB] Get:64 http://localhost:3142/debian sid/main amd64 sensible-utils all 0.0.20 [19.3 kB] Get:65 http://localhost:3142/debian sid/main amd64 libmagic-mgc amd64 1:5.45-2+b1 [314 kB] Get:66 http://localhost:3142/debian sid/main amd64 libmagic1 amd64 1:5.45-2+b1 [105 kB] Get:67 http://localhost:3142/debian sid/main amd64 file amd64 1:5.45-2+b1 [43.1 kB] Get:68 http://localhost:3142/debian sid/main amd64 gettext-base amd64 0.21-14 [161 kB] Get:69 http://localhost:3142/debian sid/main amd64 libuchardet0 amd64 0.0.8-1 [68.5 kB] Get:70 http://localhost:3142/debian sid/main amd64 groff-base amd64 1.23.0-3 [1180 kB] Get:71 http://localhost:3142/debian sid/main amd64 bsdextrautils amd64 2.39.3-6 [89.4 kB] Get:72 http://localhost:3142/debian sid/main amd64 libpipeline1 amd64 1.5.7-1+b2 [38.1 kB] Get:73 http://localhost:3142/debian sid/main amd64 man-db amd64 2.12.0-1 [1402 kB] Get:74 http://localhost:3142/debian sid/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:75 http://localhost:3142/debian sid/main amd64 m4 amd64 1.4.19-4 [287 kB] Get:76 http://localhost:3142/debian sid/main amd64 autoconf all 2.71-3 [332 kB] Get:77 http://localhost:3142/debian sid/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:78 http://localhost:3142/debian sid/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:79 http://localhost:3142/debian sid/main amd64 autopoint all 0.21-14 [496 kB] Get:80 http://localhost:3142/debian sid/main amd64 binutils-aarch64-linux-gnu amd64 2.41.50.20231227-1 [3371 kB] Get:81 http://localhost:3142/debian sid/main amd64 gcc-13-aarch64-linux-gnu-base amd64 13.2.0-7cross2 [41.0 kB] Get:82 http://localhost:3142/debian sid/main amd64 cpp-13-aarch64-linux-gnu amd64 13.2.0-7cross2 [9771 kB] Get:83 http://localhost:3142/debian sid/main amd64 cpp-aarch64-linux-gnu amd64 4:13.2.0-2 [4164 B] Get:84 http://localhost:3142/debian sid/main amd64 cross-config all 2.6.20 [16.3 kB] Get:85 http://localhost:3142/debian sid/main amd64 gcc-13-cross-base all 13.2.0-7cross2 [36.6 kB] Get:86 http://localhost:3142/debian sid/main amd64 libc6-arm64-cross all 2.37-12cross1 [1006 kB] Get:87 http://localhost:3142/debian sid/main amd64 libgcc-s1-arm64-cross all 13.2.0-7cross2 [40.8 kB] Get:88 http://localhost:3142/debian sid/main amd64 libgomp1-arm64-cross all 13.2.0-7cross2 [112 kB] Get:89 http://localhost:3142/debian sid/main amd64 libitm1-arm64-cross all 13.2.0-7cross2 [23.3 kB] Get:90 http://localhost:3142/debian sid/main amd64 libatomic1-arm64-cross all 13.2.0-7cross2 [9892 B] Get:91 http://localhost:3142/debian sid/main amd64 libasan8-arm64-cross all 13.2.0-7cross2 [2407 kB] Get:92 http://localhost:3142/debian sid/main amd64 liblsan0-arm64-cross all 13.2.0-7cross2 [1068 kB] Get:93 http://localhost:3142/debian sid/main amd64 libtsan2-arm64-cross all 13.2.0-7cross2 [2278 kB] Get:94 http://localhost:3142/debian sid/main amd64 libstdc++6-arm64-cross all 13.2.0-7cross2 [575 kB] Get:95 http://localhost:3142/debian sid/main amd64 libubsan1-arm64-cross all 13.2.0-7cross2 [980 kB] Get:96 http://localhost:3142/debian sid/main amd64 libhwasan0-arm64-cross all 13.2.0-7cross2 [1119 kB] Get:97 http://localhost:3142/debian sid/main amd64 libgcc-13-dev-arm64-cross all 13.2.0-7cross2 [2226 kB] Get:98 http://localhost:3142/debian sid/main amd64 gcc-13-aarch64-linux-gnu amd64 13.2.0-7cross2 [19.2 MB] Get:99 http://localhost:3142/debian sid/main amd64 gcc-aarch64-linux-gnu amd64 4:13.2.0-2 [1468 B] Get:100 http://localhost:3142/debian sid/main amd64 linux-libc-dev-arm64-cross all 6.5.8-1cross1 [1990 kB] Get:101 http://localhost:3142/debian sid/main amd64 libc6-dev-arm64-cross all 2.37-12cross1 [1427 kB] Get:102 http://localhost:3142/debian sid/main amd64 libstdc++-13-dev-arm64-cross all 13.2.0-7cross2 [2138 kB] Get:103 http://localhost:3142/debian sid/main amd64 g++-13-aarch64-linux-gnu amd64 13.2.0-7cross2 [10.7 MB] Get:104 http://localhost:3142/debian sid/main amd64 g++-aarch64-linux-gnu amd64 4:13.2.0-2 [1176 B] Get:105 http://localhost:3142/debian sid/main amd64 libconfig-inifiles-perl all 3.000003-2 [45.9 kB] Get:106 http://localhost:3142/debian sid/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get:107 http://localhost:3142/debian sid/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:108 http://localhost:3142/debian sid/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get:109 http://localhost:3142/debian sid/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:110 http://localhost:3142/debian sid/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-1+b1 [322 kB] Get:111 http://localhost:3142/debian sid/main amd64 libxml-simple-perl all 2.25-2 [69.8 kB] Get:112 http://localhost:3142/debian sid/main amd64 libyaml-perl all 1.31-1 [64.8 kB] Get:113 http://localhost:3142/debian sid/main amd64 libconfig-auto-perl all 0.44-2 [19.2 kB] Get:114 http://localhost:3142/debian sid/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get:115 http://localhost:3142/debian sid/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get:116 http://localhost:3142/debian sid/main amd64 libdebian-dpkgcross-perl all 2.6.20 [15.3 kB] Get:117 http://localhost:3142/debian sid/main amd64 dpkg-cross all 2.6.20 [25.8 kB] Get:118 http://localhost:3142/debian sid/main amd64 crossbuild-essential-arm64 all 12.10 [3484 B] Get:119 http://localhost:3142/debian sid/main amd64 libdebhelper-perl all 13.11.9 [82.3 kB] Get:120 http://localhost:3142/debian sid/main amd64 libtool all 2.4.7-7 [517 kB] Get:121 http://localhost:3142/debian sid/main amd64 dh-autoreconf all 20 [17.1 kB] Get:122 http://localhost:3142/debian sid/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:123 http://localhost:3142/debian sid/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get:124 http://localhost:3142/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get:125 http://localhost:3142/debian sid/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get:126 http://localhost:3142/debian sid/main amd64 libelf1 amd64 0.190-1+b1 [176 kB] Get:127 http://localhost:3142/debian sid/main amd64 dwz amd64 0.15-1 [109 kB] Get:128 http://localhost:3142/debian sid/main amd64 gettext amd64 0.21-14 [1300 kB] Get:129 http://localhost:3142/debian sid/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:130 http://localhost:3142/debian sid/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:131 http://localhost:3142/debian sid/main amd64 debhelper all 13.11.9 [956 kB] Get:132 http://localhost:3142/debian sid/main amd64 xml-core all 0.19 [20.1 kB] Get:133 http://localhost:3142/debian sid/main amd64 sgml-data all 2.0.11+nmu1 [179 kB] Get:134 http://localhost:3142/debian sid/main amd64 docbook all 4.5-10 [131 kB] Get:135 http://localhost:3142/debian sid/main amd64 libosp5 amd64 1.5.2-14 [933 kB] Get:136 http://localhost:3142/debian sid/main amd64 opensp amd64 1.5.2-14 [418 kB] Get:137 http://localhost:3142/debian sid/main amd64 docbook-to-man amd64 1:2.0.0-45 [77.4 kB] Get:138 http://localhost:3142/debian sid/main amd64 fonts-lmodern all 2.005-1 [4540 kB] Get:139 http://localhost:3142/debian sid/main arm64 gcc-11-base arm64 11.4.0-7 [40.3 kB] Get:140 http://localhost:3142/debian sid/main arm64 gcc-13-base arm64 13.2.0-9 [41.5 kB] Get:141 http://localhost:3142/debian sid/main amd64 libgs-common all 10.02.1~dfsg-2 [148 kB] Get:142 http://localhost:3142/debian sid/main amd64 libgs10-common all 10.02.1~dfsg-2 [474 kB] Get:143 http://localhost:3142/debian sid/main amd64 libavahi-common-data amd64 0.8-13+b1 [111 kB] Get:144 http://localhost:3142/debian sid/main amd64 libavahi-common3 amd64 0.8-13+b1 [43.3 kB] Get:145 http://localhost:3142/debian sid/main amd64 libdbus-1-3 amd64 1.14.10-3+b1 [204 kB] Get:146 http://localhost:3142/debian sid/main amd64 libavahi-client3 amd64 0.8-13+b1 [47.1 kB] Get:147 http://localhost:3142/debian sid/main amd64 libcups2 amd64 2.4.7-1+b1 [247 kB] Get:148 http://localhost:3142/debian sid/main amd64 libidn12 amd64 1.41-1 [83.8 kB] Get:149 http://localhost:3142/debian sid/main amd64 libijs-0.35 amd64 0.35-15.1 [14.8 kB] Get:150 http://localhost:3142/debian sid/main amd64 libjbig2dec0 amd64 0.20-1 [64.0 kB] Get:151 http://localhost:3142/debian sid/main amd64 libpaper1 amd64 1.1.29 [12.5 kB] Get:152 http://localhost:3142/debian sid/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get:153 http://localhost:3142/debian sid/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get:154 http://localhost:3142/debian sid/main amd64 libxt6 amd64 1:1.2.1-1.1 [186 kB] Get:155 http://localhost:3142/debian sid/main amd64 libgs10 amd64 10.02.1~dfsg-2 [2502 kB] Get:156 http://localhost:3142/debian sid/main amd64 ghostscript amd64 10.02.1~dfsg-2 [49.6 kB] Get:157 http://localhost:3142/debian sid/main amd64 libnetpbm11 amd64 2:11.04.05-2 [177 kB] Get:158 http://localhost:3142/debian sid/main amd64 netpbm amd64 2:11.04.05-2 [2038 kB] Get:159 http://localhost:3142/debian sid/main amd64 tex-common all 6.18 [32.5 kB] Get:160 http://localhost:3142/debian sid/main amd64 libpaper-utils amd64 1.1.29 [8868 B] Get:161 http://localhost:3142/debian sid/main amd64 libkpathsea6 amd64 2023.20230311.66589-8 [154 kB] Get:162 http://localhost:3142/debian sid/main amd64 libptexenc1 amd64 2023.20230311.66589-8 [46.8 kB] Get:163 http://localhost:3142/debian sid/main amd64 libsynctex2 amd64 2023.20230311.66589-8 [61.7 kB] Get:164 http://localhost:3142/debian sid/main amd64 libtexlua53-5 amd64 2023.20230311.66589-8 [113 kB] Get:165 http://localhost:3142/debian sid/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get:166 http://localhost:3142/debian sid/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB] Get:167 http://localhost:3142/debian sid/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get:168 http://localhost:3142/debian sid/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get:169 http://localhost:3142/debian sid/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get:170 http://localhost:3142/debian sid/main amd64 libcairo2 amd64 1.18.0-1+b1 [531 kB] Get:171 http://localhost:3142/debian sid/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get:172 http://localhost:3142/debian sid/main amd64 libharfbuzz0b amd64 8.0.1-1+b2 [2161 kB] Get:173 http://localhost:3142/debian sid/main amd64 libpotrace0 amd64 1.16-2 [26.2 kB] Get:174 http://localhost:3142/debian sid/main amd64 libteckit0 amd64 2.5.11+ds1-1+b1 [335 kB] Get:175 http://localhost:3142/debian sid/main amd64 libxmu6 amd64 2:1.1.3-3 [60.1 kB] Get:176 http://localhost:3142/debian sid/main amd64 libxpm4 amd64 1:3.5.17-1 [55.8 kB] Get:177 http://localhost:3142/debian sid/main amd64 libxaw7 amd64 2:1.0.14-1 [201 kB] Get:178 http://localhost:3142/debian sid/main amd64 libxi6 amd64 2:1.8-1+b1 [84.2 kB] Get:179 http://localhost:3142/debian sid/main amd64 libzzip-0-13 amd64 0.13.72+dfsg.1-1.1 [58.3 kB] Get:180 http://localhost:3142/debian sid/main amd64 texlive-binaries amd64 2023.20230311.66589-8 [8494 kB] Get:181 http://localhost:3142/debian sid/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:182 http://localhost:3142/debian sid/main amd64 texlive-base all 2023.20231207-1 [22.0 MB] Get:183 http://localhost:3142/debian sid/main amd64 hicolor-icon-theme all 0.17-2 [11.4 kB] Get:184 http://localhost:3142/debian sid/main amd64 imagemagick-6.q16 amd64 8:6.9.12.98+dfsg1-5 [289 kB] Get:185 http://localhost:3142/debian sid/main amd64 imagemagick amd64 8:6.9.12.98+dfsg1-5 [19.2 kB] Get:186 http://localhost:3142/debian sid/main amd64 hevea amd64 2.36-2+b1 [1892 kB] Get:187 http://localhost:3142/debian sid/main arm64 libgcc-s1 arm64 13.2.0-9 [40.9 kB] Get:188 http://localhost:3142/debian sid/main arm64 libc6 arm64 2.37-13 [2316 kB] Get:189 http://localhost:3142/debian sid/main arm64 libasan6 arm64 11.4.0-7 [1951 kB] Get:190 http://localhost:3142/debian sid/main arm64 libatomic1 arm64 13.2.0-9 [10.2 kB] Get:191 http://localhost:3142/debian sid/main arm64 libblkid1 arm64 2.39.3-6 [155 kB] Get:192 http://localhost:3142/debian sid/main arm64 libcrypt1 arm64 1:4.4.36-4 [90.5 kB] Get:193 http://localhost:3142/debian sid/main arm64 libcrypt-dev arm64 1:4.4.36-4 [121 kB] Get:194 http://localhost:3142/debian sid/main arm64 libkrb5support0 arm64 1.20.1-5 [32.5 kB] Get:195 http://localhost:3142/debian sid/main arm64 libcom-err2 arm64 1.47.0-2+b1 [19.9 kB] Get:196 http://localhost:3142/debian sid/main arm64 libk5crypto3 arm64 1.20.1-5 [79.9 kB] Get:197 http://localhost:3142/debian sid/main arm64 libkeyutils1 arm64 1.6.3-2+b2 [9296 B] Get:198 http://localhost:3142/debian sid/main arm64 libssl3 arm64 3.1.4-2 [1835 kB] Get:199 http://localhost:3142/debian sid/main arm64 libkrb5-3 arm64 1.20.1-5 [315 kB] Get:200 http://localhost:3142/debian sid/main arm64 libgssapi-krb5-2 arm64 1.20.1-5 [124 kB] Get:201 http://localhost:3142/debian sid/main arm64 libtirpc3 arm64 1.3.4+ds-1 [77.9 kB] Get:202 http://localhost:3142/debian sid/main arm64 libnsl2 arm64 1.3.0-3 [37.5 kB] Get:203 http://localhost:3142/debian sid/main arm64 libtirpc-dev arm64 1.3.4+ds-1 [192 kB] Get:204 http://localhost:3142/debian sid/main arm64 libnsl-dev arm64 1.3.0-3 [66.3 kB] Get:205 http://localhost:3142/debian sid/main arm64 libc6-dev arm64 2.37-13 [1433 kB] Get:206 http://localhost:3142/debian sid/main arm64 libuuid1 arm64 2.39.3-6 [29.4 kB] Get:207 http://localhost:3142/debian sid/main arm64 uuid-dev arm64 2.39.3-6 [41.7 kB] Get:208 http://localhost:3142/debian sid/main arm64 libblkid-dev arm64 2.39.3-6 [199 kB] Get:209 http://localhost:3142/debian sid/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB] Get:210 http://localhost:3142/debian sid/main arm64 libffi8 arm64 3.4.4-2 [20.8 kB] Get:211 http://localhost:3142/debian sid/main arm64 libffi-dev arm64 3.4.4-2 [56.8 kB] Get:212 http://localhost:3142/debian sid/main arm64 libgomp1 arm64 13.2.0-9 [118 kB] Get:213 http://localhost:3142/debian sid/main arm64 libitm1 arm64 13.2.0-9 [23.9 kB] Get:214 http://localhost:3142/debian sid/main arm64 liblsan0 arm64 13.2.0-9 [1069 kB] Get:215 http://localhost:3142/debian sid/main arm64 libtsan0 arm64 11.4.0-7 [1957 kB] Get:216 http://localhost:3142/debian sid/main arm64 libstdc++6 arm64 13.2.0-9 [622 kB] Get:217 http://localhost:3142/debian sid/main arm64 libubsan1 arm64 13.2.0-9 [981 kB] Get:218 http://localhost:3142/debian sid/main arm64 libhwasan0 arm64 13.2.0-9 [1120 kB] Get:219 http://localhost:3142/debian sid/main arm64 libgcc-11-dev arm64 11.4.0-7 [935 kB] Get:220 http://localhost:3142/debian sid/main arm64 libpcre2-8-0 arm64 10.42-4 [231 kB] Get:221 http://localhost:3142/debian sid/main arm64 libselinux1 arm64 3.5-1+b2 [70.0 kB] Get:222 http://localhost:3142/debian sid/main arm64 libmount1 arm64 2.39.3-6 [182 kB] Get:223 http://localhost:3142/debian sid/main arm64 zlib1g arm64 1:1.3.dfsg-3 [83.7 kB] Get:224 http://localhost:3142/debian sid/main arm64 libglib2.0-0 arm64 2.78.3-1 [1361 kB] Get:225 http://localhost:3142/debian sid/main amd64 libglib2.0-data all 2.78.3-1 [1223 kB] Get:226 http://localhost:3142/debian sid/main amd64 libglib2.0-bin amd64 2.78.3-1 [115 kB] Get:227 http://localhost:3142/debian sid/main amd64 python3-lib2to3 all 3.11.5-1 [77.5 kB] Get:228 http://localhost:3142/debian sid/main amd64 python3-distutils all 3.11.5-1 [131 kB] Get:229 http://localhost:3142/debian sid/main amd64 libglib2.0-dev-bin amd64 2.78.3-1 [157 kB] Get:230 http://localhost:3142/debian sid/main arm64 libsepol2 arm64 3.5-2 [249 kB] Get:231 http://localhost:3142/debian sid/main arm64 libsepol-dev arm64 3.5-2 [335 kB] Get:232 http://localhost:3142/debian sid/main arm64 libpcre2-16-0 arm64 10.42-4 [216 kB] Get:233 http://localhost:3142/debian sid/main arm64 libpcre2-32-0 arm64 10.42-4 [206 kB] Get:234 http://localhost:3142/debian sid/main arm64 libpcre2-posix3 arm64 10.42-4 [55.6 kB] Get:235 http://localhost:3142/debian sid/main arm64 libpcre2-dev arm64 10.42-4 [668 kB] Get:236 http://localhost:3142/debian sid/main arm64 libselinux1-dev arm64 3.5-1+b2 [161 kB] Get:237 http://localhost:3142/debian sid/main arm64 libmount-dev arm64 2.39.3-6 [23.6 kB] Get:238 http://localhost:3142/debian sid/main amd64 libpkgconf3 amd64 1.8.1-1+b2 [36.4 kB] Get:239 http://localhost:3142/debian sid/main amd64 pkgconf-bin amd64 1.8.1-1+b2 [29.7 kB] Get:240 http://localhost:3142/debian sid/main arm64 pkgconf arm64 1.8.1-1+b2 [26.2 kB] Get:241 http://localhost:3142/debian sid/main arm64 pkg-config arm64 1.8.1-1+b2 [14.0 kB] Get:242 http://localhost:3142/debian sid/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3 [915 kB] Get:243 http://localhost:3142/debian sid/main arm64 libglib2.0-dev arm64 2.78.3-1 [1660 kB] Get:244 http://localhost:3142/debian sid/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:245 http://localhost:3142/debian sid/main amd64 libmime-charset-perl all 1.013.1-2 [34.0 kB] Get:246 http://localhost:3142/debian sid/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:247 http://localhost:3142/debian sid/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB] Get:248 http://localhost:3142/debian sid/main amd64 libsombok3 amd64 2.4.0-2+b1 [31.4 kB] Get:249 http://localhost:3142/debian sid/main arm64 libstdc++-11-dev arm64 11.4.0-7 [1942 kB] Get:250 http://localhost:3142/debian sid/main amd64 libunicode-linebreak-perl amd64 0.0.20190101-1+b5 [97.8 kB] Get:251 http://localhost:3142/debian sid/main amd64 libyaml-tiny-perl all 1.74-1 [30.7 kB] Get:252 http://localhost:3142/debian sid/main amd64 lmodern all 2.005-1 [9480 kB] Get:253 http://localhost:3142/debian sid/main amd64 texlive-latex-base all 2023.20231207-1 [1248 kB] Get:254 http://localhost:3142/debian sid/main amd64 texlive-luatex all 2023.20231207-1 [25.6 MB] Get:255 http://localhost:3142/debian sid/main amd64 texlive-plain-generic all 2023.20231207-3 [28.9 MB] Get:256 http://localhost:3142/debian sid/main amd64 texlive-extra-utils all 2023.20231207-3 [63.3 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 319 MB in 2s (180 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 16249 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-6_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-6) ... Selecting previously unselected package libfftw3-double3:amd64. Preparing to unpack .../01-libfftw3-double3_3.3.10-1_amd64.deb ... Unpacking libfftw3-double3:amd64 (3.3.10-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../02-libexpat1_2.5.0-2+b2_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-2+b2) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../03-libbrotli1_1.1.0-2+b3_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b3) ... Selecting previously unselected package libpng16-16:amd64. Preparing to unpack .../04-libpng16-16_1.6.40-3_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.40-3) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../05-libfreetype6_2.13.2+dfsg-1+b1_amd64.deb ... 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Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel All runlevel operations denied by policy invoke-rc.d: policy-rc.d denied execution of restart. Setting up libmagic1:amd64 (1:5.45-2+b1) ... Setting up libnetpbm11:amd64 (2:11.04.05-2) ... Setting up libdeflate0:amd64 (1.18-1) ... Setting up libxml-namespacesupport-perl (1.12-2) ... Setting up gettext-base (0.21-14) ... Setting up m4 (1.4.19-4) ... Setting up binutils-aarch64-linux-gnu (2.41.50.20231227-1) ... Setting up libzzip-0-13:amd64 (0.13.72+dfsg.1-1.1) ... Setting up file (1:5.45-2+b1) ... Setting up libyaml-perl (1.31-1) ... Setting up libyaml-tiny-perl (1.74-1) ... Setting up libjbig0:amd64 (2.1-6.1) ... Setting up poppler-data (0.4.12-1) ... Setting up libosp5 (1.5.2-14) ... Setting up libxml-sax-base-perl (1.09-3) ... Setting up libio-string-perl (1.08-4) ... Setting up libfontenc1:amd64 (1:1.1.4-1+b2) ... Setting up autotools-dev (20220109.1) ... Setting up libglib2.0-data (2.78.3-1) ... Setting up cross-config (2.6.20) ... Setting up libpkgconf3:amd64 (1.8.1-1+b2) ... Setting up gcc-13-base:arm64 (13.2.0-9) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-2+b2) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libjbig2dec0:amd64 (0.20-1) ... Setting up libteckit0:amd64 (2.5.11+ds1-1+b1) ... Setting up libavahi-common-data:amd64 (0.8-13+b1) ... Setting up gcc-13-cross-base (13.2.0-7cross2) ... Setting up libdbus-1-3:amd64 (1.14.10-3+b1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libc6-arm64-cross (2.37-12cross1) ... Setting up t1utils (1.41-4) ... Setting up libtexlua53-5:amd64 (2023.20230311.66589-8) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16:amd64 (1.6.40-3) ... Setting up libidn12:amd64 (1.41-1) ... Setting up autopoint (0.21-14) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libitm1-arm64-cross (13.2.0-7cross2) ... Setting up pkgconf-bin (1.8.1-1+b2) ... Setting up libncursesw6:amd64 (6.4+20231209-1) ... Setting up libltdl7:amd64 (2.4.7-7) ... Setting up libfftw3-double3:amd64 (3.3.10-1) ... Setting up libkpathsea6:amd64 (2023.20230311.66589-8) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:amd64 (1.3.2-0.3) ... Setting up linux-libc-dev-arm64-cross (6.5.8-1cross1) ... Setting up libdav1d7:amd64 (1.3.0-2+b1) ... Setting up liblqr-1-0:amd64 (0.4.2-2.1) ... Setting up sensible-utils (0.0.20) ... Setting up libmime-charset-perl (1.013.1-2) ... Setting up libtiff6:amd64 (4.5.1+git230720-3) ... Setting up libuchardet0:amd64 (0.0.8-1) ... Setting up fonts-lmodern (2.005-1) ... Setting up libopenjp2-7:amd64 (2.5.0-2+b2) ... Setting up libsub-override-perl (0.10-1) ... Setting up libthai-data (0.1.29-2) ... Setting up gcc-13-aarch64-linux-gnu-base:amd64 (13.2.0-7cross2) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libraw23:amd64 (0.21.1-7) ... Setting up libde265-0:amd64 (1.0.15-1) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up libwebpmux3:amd64 (1.3.2-0.3) ... Setting up libbsd0:amd64 (0.11.7-4) ... Setting up libelf1:amd64 (0.190-1+b1) ... Setting up readline-common (8.2-3) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b2) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up liblocale-gettext-perl (1.07-6) ... Setting up libsynctex2:amd64 (2023.20230311.66589-8) ... Setting up libgcc-s1-arm64-cross (13.2.0-7cross2) ... Setting up libpotrace0:amd64 (1.16-2) ... Setting up libatomic1-arm64-cross (13.2.0-7cross2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up liblsan0-arm64-cross (13.2.0-7cross2) ... Setting up libice6:amd64 (2:1.0.10-1) ... Setting up libgomp1-arm64-cross (13.2.0-7cross2) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libxcb1:amd64 (1.15-1) ... Setting up gettext (0.21-14) ... Setting up cpp-13-aarch64-linux-gnu (13.2.0-7cross2) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:amd64 (1.15-1) ... Setting up fontconfig-config (2.14.2-6+b1) ... Setting up libwebpdemux2:amd64 (1.3.2-0.3) ... Setting up libreadline8:amd64 (8.2-3) ... Setting up libavahi-common3:amd64 (0.8-13+b1) ... Setting up libglib2.0-bin (2.78.3-1) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libhwasan0-arm64-cross (13.2.0-7cross2) ... Setting up opensp (1.5.2-14) ... Setting up libc6-dev-arm64-cross (2.37-12cross1) ... Setting up pkgconf:arm64 (1.8.1-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libstdc++6-arm64-cross (13.2.0-7cross2) ... Setting up dh-autoreconf (20) ... Setting up libthai0:amd64 (0.1.29-2) ... Setting up cpp-aarch64-linux-gnu (4:13.2.0-2) ... Setting up libptexenc1:amd64 (2023.20230311.66589-8) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b1) ... Setting up pkg-config:arm64 (1.8.1-1+b2) ... Setting up ucf (3.0043+nmu1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... Setting up xml-core (0.19) ... Setting up libx11-6:amd64 (2:1.8.7-1) ... Setting up libharfbuzz0b:amd64 (8.0.1-1+b2) ... Setting up libfontconfig1:amd64 (2.14.2-6+b1) ... Setting up libasan8-arm64-cross (13.2.0-7cross2) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libtsan2-arm64-cross (13.2.0-7cross2) ... Setting up libavahi-client3:amd64 (0.8-13+b1) ... Setting up libpaper1:amd64 (1.1.29) ... Creating config file /etc/papersize with new version Setting up libxpm4:amd64 (1:3.5.17-1) ... Setting up libubsan1-arm64-cross (13.2.0-7cross2) ... Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up libsombok3:amd64 (2.4.0-2+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.7-2) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libpaper-utils (1.1.29) ... Setting up xfonts-utils (1:7.7+6) ... Setting up man-db (2.12.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-3) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libcairo2:amd64 (1.18.0-1+b1) ... Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libunicode-linebreak-perl (0.0.20190101-1+b5) ... Setting up netpbm (2:11.04.05-2) ... Setting up libxt6:amd64 (1:1.2.1-1.1) ... Setting up libgcc-13-dev-arm64-cross (13.2.0-7cross2) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+b1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libcups2:amd64 (2.4.7-1+b1) ... Setting up lmodern (2.005-1) ... Setting up libpython3-stdlib:amd64 (3.11.6-1) ... Setting up python3.11 (3.11.7-2) ... Setting up libxmu6:amd64 (2:1.1.3-3) ... Setting up libxi6:amd64 (2:1.8-1+b1) ... Setting up debhelper (13.11.9) ... Setting up python3 (3.11.6-1) ... Setting up libxaw7:amd64 (2:1.0.14-1) ... Setting up gcc-13-aarch64-linux-gnu (13.2.0-7cross2) ... Setting up fonts-urw-base35 (20200910-7) ... Setting up libstdc++-13-dev-arm64-cross (13.2.0-7cross2) ... Setting up libxml-simple-perl (2.25-2) ... Setting up texlive-binaries (2023.20230311.66589-8) ... 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 Setting up python3-lib2to3 (3.11.5-1) ... Setting up texlive-base (2023.20231207-1) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up python3-distutils (3.11.5-1) ... Setting up g++-13-aarch64-linux-gnu (13.2.0-7cross2) ... Setting up libgs10-common (10.02.1~dfsg-2) ... Setting up gcc-aarch64-linux-gnu (4:13.2.0-2) ... Setting up libglib2.0-dev-bin (2.78.3-1) ... Setting up texlive-luatex (2023.20231207-1) ... Setting up texlive-plain-generic (2023.20231207-3) ... Setting up libconfig-auto-perl (0.44-2) ... Setting up texlive-latex-base (2023.20231207-1) ... Setting up texlive-extra-utils (2023.20231207-3) ... Setting up g++-aarch64-linux-gnu (4:13.2.0-2) ... Setting up libdebian-dpkgcross-perl (2.6.20) ... Setting up libgs10:amd64 (10.02.1~dfsg-2) ... Setting up ghostscript (10.02.1~dfsg-2) ... Setting up dpkg-cross (2.6.20) ... Setting up crossbuild-essential-arm64 (12.10) ... Setting up libheif-plugin-dav1d:amd64 (1.17.6-1) ... Setting up libheif-plugin-libde265:amd64 (1.17.6-1) ... Setting up libheif1:amd64 (1.17.6-1) ... Setting up libgcc-s1:arm64 (13.2.0-9) ... Setting up libmagickcore-6.q16-7:amd64 (8:6.9.12.98+dfsg1-5) ... Setting up libc6:arm64 (2.37-13) ... Setting up libffi8:arm64 (3.4.4-2) ... Setting up libhwasan0:arm64 (13.2.0-9) ... Setting up libmagickwand-6.q16-7:amd64 (8:6.9.12.98+dfsg1-5) ... Setting up libblkid1:arm64 (2.39.3-6) ... Setting up libstdc++6:arm64 (13.2.0-9) ... Setting up liblsan0:arm64 (13.2.0-9) ... Setting up libitm1:arm64 (13.2.0-9) ... Setting up libtsan0:arm64 (11.4.0-7) ... Setting up libkeyutils1:arm64 (1.6.3-2+b2) ... Setting up libssl3:arm64 (3.1.4-2) ... Setting up zlib1g:arm64 (1:1.3.dfsg-3) ... Setting up libcrypt1:arm64 (1:4.4.36-4) ... Setting up libcom-err2:arm64 (1.47.0-2+b1) ... Setting up libgomp1:arm64 (13.2.0-9) ... Setting up libffi-dev:arm64 (3.4.4-2) ... Setting up libpcre2-16-0:arm64 (10.42-4) ... Setting up libasan6:arm64 (11.4.0-7) ... Setting up libkrb5support0:arm64 (1.20.1-5) ... Setting up libpcre2-32-0:arm64 (10.42-4) ... Setting up libatomic1:arm64 (13.2.0-9) ... Setting up libuuid1:arm64 (2.39.3-6) ... Setting up libsepol2:arm64 (3.5-2) ... Setting up libsepol-dev:arm64 (3.5-2) ... Setting up libpcre2-8-0:arm64 (10.42-4) ... Setting up libk5crypto3:arm64 (1.20.1-5) ... Setting up libubsan1:arm64 (13.2.0-9) ... Setting up imagemagick-6.q16 (8:6.9.12.98+dfsg1-5) ... update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare (compare) in auto mode update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare-im6 (compare-im6) in auto mode update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate (animate) in auto mode update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate-im6 (animate-im6) in auto mode update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert (convert) in auto mode update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert-im6 (convert-im6) in auto mode update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite (composite) in auto mode update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite-im6 (composite-im6) in auto mode update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure (conjure) in auto mode update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure-im6 (conjure-im6) in auto mode update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import (import) in auto mode update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import-im6 (import-im6) in auto mode update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify (identify) in auto mode update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify-im6 (identify-im6) in auto mode update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream (stream) in auto mode update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream-im6 (stream-im6) in auto mode update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display (display) in auto mode update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display-im6 (display-im6) in auto mode update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage (montage) in auto mode update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage-im6 (montage-im6) in auto mode update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify (mogrify) in auto mode update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify-im6 (mogrify-im6) in auto mode Setting up libpcre2-posix3:arm64 (10.42-4) ... Setting up libgcc-11-dev:arm64 (11.4.0-7) ... Setting up libcrypt-dev:arm64 (1:4.4.36-4) ... Setting up libkrb5-3:arm64 (1.20.1-5) ... Setting up libselinux1:arm64 (3.5-1+b2) ... Setting up libgssapi-krb5-2:arm64 (1.20.1-5) ... Setting up hevea (2.36-2+b1) ... Setting up imagemagick (8:6.9.12.98+dfsg1-5) ... Setting up libmount1:arm64 (2.39.3-6) ... Setting up libtirpc3:arm64 (1.3.4+ds-1) ... Setting up libglib2.0-0:arm64 (2.78.3-1) ... /var/lib/dpkg/info/libglib2.0-0:arm64.postinst: 42: /usr/lib/aarch64-linux-gnu/glib-2.0/glib-compile-schemas: Exec format error /var/lib/dpkg/info/libglib2.0-0:arm64.postinst: 43: /usr/lib/aarch64-linux-gnu/glib-2.0/gio-querymodules: Exec format error Setting up libtirpc-dev:arm64 (1.3.4+ds-1) ... Setting up libnsl2:arm64 (1.3.0-3) ... Setting up libnsl-dev:arm64 (1.3.0-3) ... Setting up libc6-dev:arm64 (2.37-13) ... Setting up libpcre2-dev:arm64 (10.42-4) ... Setting up libselinux1-dev:arm64 (3.5-1+b2) ... Setting up uuid-dev:arm64 (2.39.3-6) ... Setting up libstdc++-11-dev:arm64 (11.4.0-7) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg-3) ... Setting up libblkid-dev:arm64 (2.39.3-6) ... Setting up libmount-dev:arm64 (2.39.3-6) ... Setting up libglib2.0-dev:arm64 (2.78.3-1) ... Processing triggers for libc-bin (2.37-13) ... Processing triggers for sgml-base (1.31) ... Setting up sgml-data (2.0.11+nmu1) ... Processing triggers for sgml-base (1.31) ... Setting up docbook (4.5-10) ... Processing triggers for sgml-base (1.31) ... Setting up docbook-to-man (1:2.0.0-45) ... Setting up sbuild-build-depends-main-dummy:arm64 (0.invalid.0) ... Processing triggers for tex-common (6.18) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.1.0-13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.55-1 (2023-09-29) amd64 (x86_64) Toolchain package versions: binutils_2.41.50.20231227-1 dpkg-dev_1.22.2 g++-11_11.4.0-7 g++-13_13.2.0-9 gcc-11_11.4.0-7 gcc-13_13.2.0-9 libc6-dev_2.37-13 libstdc++-11-dev_11.4.0-7 libstdc++-13-dev_13.2.0-9 libstdc++-13-dev-arm64-cross_13.2.0-7cross2 libstdc++6_13.2.0-9 libstdc++6-arm64-cross_13.2.0-7cross2 linux-libc-dev_6.6.9-1 Package versions: adduser_3.137 apt_2.7.7 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13 base-passwd_3.6.3 bash_5.2.21-2 binutils_2.41.50.20231227-1 binutils-aarch64-linux-gnu_2.41.50.20231227-1 binutils-common_2.41.50.20231227-1 binutils-x86-64-linux-gnu_2.41.50.20231227-1 bsdextrautils_2.39.3-6 bsdutils_1:2.39.3-6 build-essential_12.10 bzip2_1.0.8-5+b2 coreutils_9.4-3 cpp_4:13.2.0-2 cpp-11_11.4.0-7 cpp-13_13.2.0-9 cpp-13-aarch64-linux-gnu_13.2.0-7cross2 cpp-aarch64-linux-gnu_4:13.2.0-2 cross-config_2.6.20 crossbuild-essential-arm64_12.10 dash_0.5.12-6 debconf_1.5.83 debhelper_13.11.9 debian-archive-keyring_2023.4 debianutils_5.16 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 docbook_4.5-10 docbook-to-man_1:2.0.0-45 dpkg_1.22.2 dpkg-cross_2.6.20 dpkg-dev_1.22.2 dwz_0.15-1 e2fsprogs_1.47.0-2+b1 fakeroot_1.32.2-1+b1 file_1:5.45-2+b1 findutils_4.9.0-5 fontconfig-config_2.14.2-6+b1 fonts-dejavu-core_2.37-8 fonts-dejavu-mono_2.37-8 fonts-lmodern_2.005-1 fonts-urw-base35_20200910-7 g++_4:13.2.0-2 g++-11_11.4.0-7 g++-13_13.2.0-9 g++-13-aarch64-linux-gnu_13.2.0-7cross2 g++-aarch64-linux-gnu_4:13.2.0-2 gcc_4:13.2.0-2 gcc-11_11.4.0-7 gcc-11-base_11.4.0-7 gcc-12-base_12.3.0-13 gcc-13_13.2.0-9 gcc-13-aarch64-linux-gnu_13.2.0-7cross2 gcc-13-aarch64-linux-gnu-base_13.2.0-7cross2 gcc-13-base_13.2.0-9 gcc-13-cross-base_13.2.0-7cross2 gcc-9-base_9.5.0-4 gcc-aarch64-linux-gnu_4:13.2.0-2 gettext_0.21-14 gettext-base_0.21-14 ghostscript_10.02.1~dfsg-2 gpgv_2.2.40-1.1 grep_3.11-4 groff-base_1.23.0-3 gzip_1.12-1 hevea_2.36-2+b1 hicolor-icon-theme_0.17-2 hostname_3.23+nmu1 imagemagick_8:6.9.12.98+dfsg1-5 imagemagick-6-common_8:6.9.12.98+dfsg1-5 imagemagick-6.q16_8:6.9.12.98+dfsg1-5 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-4 libapt-pkg6.0_2.7.7 libarchive-zip-perl_1.68-1 libasan6_11.4.0-7 libasan8_13.2.0-9 libasan8-arm64-cross_13.2.0-7cross2 libatomic1_13.2.0-9 libatomic1-arm64-cross_13.2.0-7cross2 libattr1_1:2.5.1-5 libaudit-common_1:3.1.2-1 libaudit1_1:3.1.2-1 libavahi-client3_0.8-13+b1 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libxcb-shm0_1.15-1 libxcb1_1.15-1 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.4-1+b1 libxi6_2:1.8-1+b1 libxml-libxml-perl_2.0207+dfsg+really+2.0134-1+b1 libxml-namespacesupport-perl_1.12-2 libxml-sax-base-perl_1.09-3 libxml-sax-perl_1.02+dfsg-3 libxml-simple-perl_2.25-2 libxml2_2.9.14+dfsg-1.3+b2 libxmu6_2:1.1.3-3 libxpm4_1:3.5.17-1 libxrender1_1:0.9.10-1.1 libxt6_1:1.2.1-1.1 libxxhash0_0.8.2-2 libyaml-perl_1.31-1 libyaml-tiny-perl_1.74-1 libzstd1_1.5.5+dfsg2-2 libzzip-0-13_0.13.72+dfsg.1-1.1 linux-libc-dev_6.6.9-1 linux-libc-dev-arm64-cross_6.5.8-1cross1 lmodern_2.005-1 login_1:4.13+dfsg1-3+b1 logsave_1.47.0-2+b1 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.0-1 mawk_1.3.4.20231126-1 media-types_10.1.0 mount_2.39.3-6 ncurses-base_6.4+20231209-1 ncurses-bin_6.4+20231209-1 netbase_6.4 netpbm_2:11.04.05-2 opensp_1.5.2-14 passwd_1:4.13+dfsg1-3+b1 patch_2.7.6-7 perl_5.36.0-10+b1 perl-base_5.36.0-10+b1 perl-modules-5.34_5.34.0-5 perl-modules-5.36_5.36.0-10 pkg-config_1.8.1-1+b2 pkgconf_1.8.1-1+b2 pkgconf-bin_1.8.1-1+b2 po-debconf_1.0.21+nmu1 poppler-data_0.4.12-1 python3_3.11.6-1 python3-distutils_3.11.5-1 python3-lib2to3_3.11.5-1 python3-minimal_3.11.6-1 python3.11_3.11.7-2 python3.11-minimal_3.11.7-2 readline-common_8.2-3 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.20 sgml-base_1.31 sgml-data_2.0.11+nmu1 sysvinit-utils_3.08-5 t1utils_1.41-4 tar_1.35+dfsg-2 tex-common_6.18 texlive-base_2023.20231207-1 texlive-binaries_2023.20230311.66589-8 texlive-extra-utils_2023.20231207-3 texlive-latex-base_2023.20231207-1 texlive-luatex_2023.20231207-1 texlive-plain-generic_2023.20231207-3 tzdata_2023d-1 ucf_3.0043+nmu1 usrmerge_38 util-linux_2.39.3-6 util-linux-extra_2.39.3-6 uuid-dev_2.39.3-6 x11-common_1:7.7+23 xdg-utils_1.1.3-4.1 xfonts-encodings_1:1.0.4-2.2 xfonts-utils_1:7.7+6 xml-core_0.19 xz-utils_5.4.5-0.3 zlib1g_1:1.3.dfsg-3 zlib1g-dev_1:1.3.dfsg-3 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: wise Binary: wise, wise-doc, wise-data Architecture: any all Version: 2.4.1-23 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Charles Plessy , Andreas Tille Homepage: https://www.ebi.ac.uk/~birney/wise2/ Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/wise Vcs-Git: https://salsa.debian.org/med-team/wise.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 12), texlive-latex-base, texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev Package-List: wise deb science optional arch=any wise-data deb doc optional arch=all wise-doc deb doc optional arch=all Checksums-Sha1: 50215e0541ed043d2ee44463da1b1a0d5272d724 3410178 wise_2.4.1.orig.tar.gz 3a0b88d342fb1b6ac2ee20ced2dcbcdf44795439 27152 wise_2.4.1-23.debian.tar.xz Checksums-Sha256: 0aec5e30739110783517a429606249fc6c5fd0d65171c1a6d79ecc5ff81d2935 3410178 wise_2.4.1.orig.tar.gz 432297bafe4688cd3f3041e5d8897792ef1b7cd3afb7bef3d06274abf28d7772 27152 wise_2.4.1-23.debian.tar.xz Files: 9e90132c19a653831ce63b5af7f08302 3410178 wise_2.4.1.orig.tar.gz 55b2719ab85acb83f518de3c19708e95 27152 wise_2.4.1-23.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl6bJzMRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHl8Q//SYLAoXInTt3fiR2c5KDeaDzjnrsuW6MZ sUvYH9VA9f0kUA5avHcQ2GU82pZoDKRxWRW4xmLhOqUDMCfCkAnah44RDWPQeBLE lPGK1U8zn0P+XI1dWZuEtjfRuYKJwjzcAGOd0AqONrzFfzxfpc9ug1RvC0ERl/5R wBGZ6dUcjJ3uDK4klKPCVtSg6WBq+/fcCTYJiepxW0I7y1mbT70nJXuNnWtevqcV ifhlJuihR8N20fOobQM8uVhcDAFc8xqsgsc1022qhW3Lh1YR4r3hy3O849K7JG5b xt9Fj6AtHhLWwsoV2g6/k8kTrlhT4e48BwFnHaV3POGRyNfMjil5MAdomF7uOP9Q HJ8w+tmliP+ItPD24FXESngPQQtz6wMjtMC1rIFWEkznIxJW8gGfEwm78hWsP8Tz nsJT6F1s6AhXgSq5O713EY3jYDOazav59KwFPzlllOhKyO5u+Fd+M0D1SZa+XfnG GHc3fCdVoeUItIbM0nAXqMWJe4XoZiL8aTSu31Qez2UvvnFPIlv0dAXpw6+KvBzA iYR3fsQB/Ger5nXUGXed8U6G9dYKMdAToP6iBLp3L4zpc6CPNKahReiYg5VKzoC+ +NlYUFB7wjKcFBnW/Kkc7d53aHdFPHJASZfAGEIO7RjgaUqafOYhL8N4QnJSw5KI REUWZmItrSU= =K6w+ -----END PGP SIGNATURE----- gpgv: Signature made Sat Apr 18 16:13:39 2020 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./wise_2.4.1-23.dsc: no acceptable signature found dpkg-source: info: extracting wise in /<> dpkg-source: info: unpacking wise_2.4.1.orig.tar.gz dpkg-source: info: unpacking wise_2.4.1-23.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 01_welcome-csh.patch dpkg-source: info: applying 02_isnumber.patch dpkg-source: info: applying 03_doc-nodycache.patch dpkg-source: info: applying 04_wise2-pdflatex-update.patch dpkg-source: info: applying 05_glib2.patch dpkg-source: info: applying 06_getline.patch dpkg-source: info: applying 07_ld--as-needed.patch dpkg-source: info: applying 08_mayhem.patch dpkg-source: info: applying 09_dnal-add-return-statement.patch dpkg-source: info: applying 10_fix_path_to_data_files.patch dpkg-source: info: applying 11_consistent_manual_dates.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying cross.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.arm64 DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LOGNAME=crossqa OLDPWD=/home/crossqa PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SBUILD_CONFIG=/tmp/tmp.lwU8qRbjv8/sbuild.conf SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=sid-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1000 SCHROOT_GROUP=crossqa SCHROOT_SESSION_ID=sid-amd64-sbuild-0e395cfd-3c89-452e-9bc4-c899112f44cd SCHROOT_UID=1000 SCHROOT_USER=crossqa SHELL=/bin/sh USER=crossqa XDG_SESSION_CLASS=user dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -aarm64 -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package wise dpkg-buildpackage: info: source version 2.4.1-23 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Helmut Grohne dpkg-architecture: warning: specified GNU system type aarch64-linux-gnu does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/<>' /usr/bin/make -C src clean make[2]: Entering directory '/<>/src' cd external ; /usr/bin/make clean make[3]: Entering directory '/<>/src/external' (cd mott; make clean) make[4]: Entering directory '/<>/src/external/mott' rm -f *.[oa] make[4]: Leaving directory '/<>/src/external/mott' make[3]: Leaving directory '/<>/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 '/<>/src' /usr/bin/make -C debian/manpages.d clean make[2]: Entering directory '/<>/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 '/<>/debian/manpages.d' rm -f -r src/oldbin for i in dba psw dnal genomewise pswdb scanwise estwise genewise sywise genewisedb promoterwise pseudowise estwisedb; do rm -f src/models/$i; done rm -f src/network/scanwise_server rm -f docs/temp.tex rm -f docs/api.* rm -f docs/wise2.image.tex rm -f docs/*.pdf rm -f docs/*.aux rm -f docs/*.log rm -f docs/*.toc rm -f docs/*.pdf rm -f docs/*.dvi rm -f docs/*.ps rm -f docs/*.4ct rm -f docs/*.4tc rm -f docs/*.css rm -f docs/*.idv rm -f docs/*.lg rm -f docs/*.tmp rm -f docs/*.xref rm -f docs/*.haux rm -f docs/*.htoc rm -f docs/*.html rm -f -r docs/api rm -f -r docs/dynamite rm -f -r docs/wise2 dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/wise.substvars debian/wise-doc.substvars debian/wise-data.substvars debian/files rm -fr -- debian/wise/ debian/tmp/ debian/wise-doc/ debian/wise-data/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) make[1]: Leaving directory '/<>' debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build --sourcedirectory=src -- all cd src && make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=aarch64-linux-gnu-pkg-config CXX=aarch64-linux-gnu-g\+\+ CC=aarch64-linux-gnu-gcc all make[2]: Entering directory '/<>/src' (cd base ; make CC="aarch64-linux-gnu-gcc" CFLAGS="-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c `aarch64-linux-gnu-pkg-config --cflags glib-2.0`" libwisebase.a ) make[3]: Entering directory '/<>/src/base' aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include wiseconfig.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include wisestring.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include wiseerror.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include wisememman.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include wisefile.c wisefile.dy: In function ‘Wise2_myfclose’: wisefile.dy:72:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘FILE *’ [-Wformat=] 72 | fprintf(stderr,"Closing %d\n",ofp); | ^~~~~~~~~~~~~~ ~~~ | | | FILE * aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include wiserandom.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include wisetime.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include wiseoverlay.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include wisestreaminterface.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include commandline.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include linesubs.c ar ru libwisebase.a wiseconfig.o wisestring.o wiseerror.o wisememman.o wisefile.o wiserandom.o wisetime.o wiseoverlay.o wisestreaminterface.o commandline.o linesubs.o ar: `u' modifier ignored since `D' is the default (see `U') 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 '/<>/src/base' (cd HMMer2 ; make CC="aarch64-linux-gnu-gcc" CFLAGS="-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c `aarch64-linux-gnu-pkg-config --cflags glib-2.0`" libhmmer.a ) make[3]: Entering directory '/<>/src/HMMer2' aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c alphabet.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c core_algorithms.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c debug.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c emit.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c emulation.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c histogram.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c hmmio.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c mathsupport.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c masks.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c misc.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c modelmakers.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c plan7.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c plan9.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c prior.c prior.c: In function ‘P7ReadPrior’: prior.c:102:12: warning: implicit declaration of function ‘strcmp’ [-Wimplicit-function-declaration] 102 | if (strcmp(sptr, "DIRICHLET") == 0) pri->strategy = PRI_DCHLET; | ^~~~~~ prior.c:10:1: note: include ‘’ or provide a declaration of ‘strcmp’ 9 | #include "funcs.h" +++ |+#include 10 | #include "squid.h" aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c tophits.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c trace.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c aligneval.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c alignio.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c cluster.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c dayhoff.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c file.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c getopt.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c gnuregex.c gnuregex.c: In function ‘re_match_2’: gnuregex.c:3752:31: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 3752 | if ((int) old_regend[r] >= (int) regstart[r]) | ^ gnuregex.c:3752:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 3752 | if ((int) old_regend[r] >= (int) regstart[r]) | ^ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2394:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3758:19: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3758 | PUSH_FAILURE_POINT (p1 + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2397:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3758:19: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3758 | PUSH_FAILURE_POINT (p1 + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2394:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3905:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3905 | PUSH_FAILURE_POINT (p + mcnt, NULL, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2397:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3905:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3905 | PUSH_FAILURE_POINT (p + mcnt, NULL, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2394:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3958:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3958 | PUSH_FAILURE_POINT (p + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2397:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3958:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3958 | PUSH_FAILURE_POINT (p + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2482:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2482 | high_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^ gnuregex.c:4064:13: note: in expansion of macro ‘POP_FAILURE_POINT’ 4064 | POP_FAILURE_POINT (sdummy, pdummy, | ^~~~~~~~~~~~~~~~~ gnuregex.c:2485:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2485 | low_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^ gnuregex.c:4064:13: note: in expansion of macro ‘POP_FAILURE_POINT’ 4064 | POP_FAILURE_POINT (sdummy, pdummy, | ^~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2394:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:4097:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 4097 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2397:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:4097:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 4097 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2394:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2394 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:4110:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 4110 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2315 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2397:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2397 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:4110:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 4110 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2482:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2482 | high_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^ gnuregex.c:4278:11: note: in expansion of macro ‘POP_FAILURE_POINT’ 4278 | POP_FAILURE_POINT (d, p, | ^~~~~~~~~~~~~~~~~ gnuregex.c:2485:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2485 | low_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^ gnuregex.c:4278:11: note: in expansion of macro ‘POP_FAILURE_POINT’ 4278 | POP_FAILURE_POINT (d, p, | ^~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c interleaved.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c iupac.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c msf.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c revcomp.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c selex.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c sqerror.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c sqio.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c sre_ctype.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c sre_math.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c sre_string.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c stack.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c translate.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c types.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -c weight.c ar rcv libhmmer.a alphabet.o core_algorithms.o debug.o emit.o emulation.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o prior.o tophits.o trace.o aligneval.o alignio.o cluster.o dayhoff.o file.o getopt.o gnuregex.o interleaved.o iupac.o msf.o revcomp.o selex.o sqerror.o sqio.o sre_ctype.o sre_math.o sre_string.o stack.o translate.o types.o weight.o a - alphabet.o a - core_algorithms.o a - debug.o a - emit.o a - emulation.o a - histogram.o a - hmmio.o a - mathsupport.o a - masks.o a - misc.o a - modelmakers.o a - plan7.o a - plan9.o a - prior.o a - tophits.o a - trace.o a - aligneval.o a - alignio.o a - cluster.o a - dayhoff.o a - file.o a - getopt.o a - gnuregex.o a - interleaved.o a - iupac.o a - msf.o a - revcomp.o a - selex.o a - sqerror.o a - sqio.o a - sre_ctype.o a - sre_math.o a - sre_string.o a - stack.o a - translate.o a - types.o a - weight.o if test -x /bin/ranlib; then /bin/ranlib libhmmer.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libhmmer.a; else exit 0; fi if test -x ranlib; then ranlib libhmmer.a; else exit 0; fi chmod 644 libhmmer.a make[3]: Leaving directory '/<>/src/HMMer2' (cd dynlibsrc ; make CC="aarch64-linux-gnu-gcc" CFLAGS="-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c `aarch64-linux-gnu-pkg-config --cflags glib-2.0`" libdyna.a ) make[3]: Entering directory '/<>/src/dynlibsrc' aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ packaln.c packaln.dy: In function ‘Wise2_read_simple_PackAln’: packaln.dy:88:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 88 | fgets(buffer,MAXLINE,ifp); | ^~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ aln.c aln.dy: In function ‘Wise2_mapped_ascii_AlnBlock’: aln.dy:867:19: warning: too many arguments for format [-Wformat-extra-args] 867 | fprintf(ofp," {%3.2f} ",(double)(*score_to_double)(cuml),cuml); | ^~~~~~~~~~~~ aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ dnamatrix.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ probability.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ alnrange.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ alnconvert.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ basematrix.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ shattermatrix.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ matrixdebug.c matrixdebug.dy: In function ‘Wise2_user_DebugMatrix’: matrixdebug.dy:208:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 208 | fgets(buffer,MAXLINE,in); | ^~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ dpenvelope.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ dbsearchimpl.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ dprunimpl.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ complexsequence.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ complexevalset.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ complexconsensi.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ sequence.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ sequencestream.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ seqalign.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ hitlist.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ hsp.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ hspstream.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ codon.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ compmat.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ codonmatrix.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ codonmapper.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ sequencedb.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ hscore.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ seqlookup.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ arrayseqlookup.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ genericindexresult.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ linkedlist_lookpos.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ singlenumberspace.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ histogram.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ searchstatinterface.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ searchstatlookup.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ proteindb.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ protein.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ pairbase.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ pairbaseseq.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ genomicdb.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ randommodel.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ randomdb.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ genomic.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ cdna.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ cdnadb.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ dna.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ embl.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ genomicregion.c genomicregion.dy: In function ‘Wise2_read_EMBL_FT_into_GenomicRegion’: genomicregion.dy:756:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 756 | fgets(buffer,maxlen,ifp); | ^~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ gene.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ transcript.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ translation.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ btcanvas.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ asciibtcanvas.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ dynlibcross.c ar ru libdyna.a packaln.o aln.o dnamatrix.o probability.o alnrange.o alnconvert.o basematrix.o shattermatrix.o matrixdebug.o dpenvelope.o dbsearchimpl.o dprunimpl.o complexsequence.o complexevalset.o complexconsensi.o sequence.o sequencestream.o seqalign.o hitlist.o hsp.o hspstream.o codon.o compmat.o codonmatrix.o codonmapper.o sequencedb.o hscore.o seqlookup.o arrayseqlookup.o genericindexresult.o linkedlist_lookpos.o singlenumberspace.o histogram.o searchstatinterface.o searchstatlookup.o proteindb.o protein.o pairbase.o pairbaseseq.o genomicdb.o randommodel.o randomdb.o genomic.o cdna.o cdnadb.o dna.o embl.o genomicregion.o gene.o transcript.o translation.o btcanvas.o asciibtcanvas.o dynlibcross.o ar: `u' modifier ignored since `D' is the default (see `U') 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 '/<>/src/dynlibsrc' (cd dynlibsrc ; make CC="aarch64-linux-gnu-gcc" CFLAGS="-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c `aarch64-linux-gnu-pkg-config --cflags glib-2.0`" libdyna_glib.a ) make[3]: Entering directory '/<>/src/dynlibsrc' aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ subseqhash.c subseqhash.dy: In function ‘Wise2_is_populated_subseqhash_ghash’: subseqhash.dy:111:29: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 111 | if( g_hash_table_lookup(h,(gconstpointer)seq_number) == NULL ) { | ^ subseqhash.dy: In function ‘Wise2_lookup_subseqhash_ghash’: subseqhash.dy:128:85: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 128 | return new_linkedl_SeqLookupResultInterface((SeqLookupPos *)g_hash_table_lookup(h,(gconstpointer)seq_number)); | ^ subseqhash.dy: In function ‘Wise2_add_seq_subseqhash_ghash’: subseqhash.dy:160:54: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 160 | if((ret = (SeqLookupPos *) g_hash_table_lookup(h,(gconstpointer)seq_number)) == NULL ) { | ^ subseqhash.dy:161:29: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 161 | g_hash_table_insert(h,(gpointer)seq_number,p); | ^ subseqhash.dy: In function ‘Wise2_add_direct_number_subseqhash_ghash’: subseqhash.dy:188:52: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 188 | if((ret = (SeqLookupPos *) g_hash_table_lookup(h,(gconstpointer)seq_number)) == NULL ) { | ^ subseqhash.dy:189:27: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 189 | g_hash_table_insert(h,(gpointer)seq_number,p); | ^ aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ intallocator.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ proteinstreamedindex.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ shadowseq.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ shadowseqindex.c shadowseqindex.dy: In function ‘Wise2_dump_stats_ShadowSequenceIndex’: shadowseqindex.dy:285:15: warning: format ‘%f’ expects argument of type ‘double’, but argument 4 has type ‘long unsigned int’ [-Wformat=] 285 | fprintf(ofp,"Head memory %d [%.2f Mbytes]\n",total_head,(total_head*sizeof(ShadowArraySeqHead))/100000); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | long unsigned int aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ hsphandler.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ hspscaninterface.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ hsp2hitscan.c hsp2hitscan.dy: In function ‘Wise2_one_off_two_hit_HSPscan_query_direct’: hsp2hitscan.dy:209:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 210 | use.ru_utime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:209:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 210 | use.ru_utime.tv_sec, 211 | use.ru_utime.tv_sec/1000, | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:209:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 212 | use.ru_stime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:209:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 209 | fprintf(stderr,"START %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 213 | use.ru_stime.tv_sec/1000 | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:273:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 274 | use.ru_utime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:273:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 274 | use.ru_utime.tv_sec, 275 | use.ru_utime.tv_sec/1000, | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:273:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 276 | use.ru_stime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:273:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 273 | fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 277 | use.ru_stime.tv_sec/1000 | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:286:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 287 | use.ru_utime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:286:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 287 | use.ru_utime.tv_sec, 288 | use.ru_utime.tv_sec/1000, | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:286:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 289 | use.ru_stime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:286:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 286 | fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 290 | use.ru_stime.tv_sec/1000 | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:302:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 303 | use.ru_utime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:302:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 303 | use.ru_utime.tv_sec, 304 | use.ru_utime.tv_sec/1000, | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:302:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 305 | use.ru_stime.tv_sec, | ~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} hsp2hitscan.dy:302:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘__time_t’ {aka ‘long int’} [-Wformat=] 302 | fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ...... 306 | use.ru_stime.tv_sec/1000 | ~~~~~~~~~~~~~~~~~~~~~~~~ | | | __time_t {aka long int} aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ hsplookupscan.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ hsplookupthreaded.c hsplookupthreaded.dy: In function ‘Wise2_one_off_ordered_HSPscan_scan_query_direct’: hsplookupthreaded.dy:263:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=] 263 | fprintf(stderr,"retrieved array with %d elements\n",current_oph); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ | | | long int aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ hspthreadeddb.c hspthreadeddb.dy: In function ‘Wise2_threadeddb_scan_worker’: hspthreadeddb.dy:154:77: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 154 | fprintf(stderr,"For segment %d, finished query with %d (%d) linear\n",seg,(int)seg->lm,seg->lm->len); | ^ hspthreadeddb.dy:154:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Wise2_HSPDatabaseSegment *’ [-Wformat=] 154 | fprintf(stderr,"For segment %d, finished query with %d (%d) linear\n",seg,(int)seg->lm,seg->lm->len); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ | | | Wise2_HSPDatabaseSegment * aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ hspscanruntime.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ hsptwohitscan.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ proteinindexcons.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ dnaindexcons.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ staticseq.c ar ru libdyna_glib.a subseqhash.o intallocator.o proteinstreamedindex.o shadowseq.o shadowseqindex.o hsphandler.o hspscaninterface.o hsp2hitscan.o hsplookupscan.o hsplookupthreaded.o hspthreadeddb.o hspscanruntime.o hsptwohitscan.o proteinindexcons.o dnaindexcons.o staticseq.o ar: `u' modifier ignored since `D' is the default (see `U') 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 '/<>/src/dynlibsrc' (cd external ; make CC="aarch64-linux-gnu-gcc" CFLAGS="-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c `aarch64-linux-gnu-pkg-config --cflags glib-2.0`" all ) make[3]: Entering directory '/<>/src/external' (cd mott; make CC="aarch64-linux-gnu-gcc" CFLAGS="-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include " all) make[4]: Entering directory '/<>/src/external/mott' aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mott_api.o mott_api.c mott_api.c: In function ‘InitPvaluesMott’: mott_api.c:64:3: warning: implicit declaration of function ‘free’ [-Wimplicit-function-declaration] 64 | free(freq0); | ^~~~ mott_api.c:5:1: note: include ‘’ or provide a declaration of ‘free’ 4 | #include"gapstat.h" +++ |+#include 5 | mott_api.c:64:3: warning: incompatible implicit declaration of built-in function ‘free’ [-Wbuiltin-declaration-mismatch] 64 | free(freq0); | ^~~~ mott_api.c:64:3: note: include ‘’ or provide a declaration of ‘free’ mott_api.c: In function ‘SW_PValueMott’: mott_api.c:104:7: warning: incompatible implicit declaration of built-in function ‘free’ [-Wbuiltin-declaration-mismatch] 104 | free(freqA); | ^~~~ mott_api.c:104:7: note: include ‘’ or provide a declaration of ‘free’ mott_api.c: In function ‘KarlinAltschulStatistics2’: mott_api.c:144:5: warning: incompatible implicit declaration of built-in function ‘free’ [-Wbuiltin-declaration-mismatch] 144 | free(h+hmin); | ^~~~ mott_api.c:144:5: note: include ‘’ or provide a declaration of ‘free’ mott_api.c:155:5: warning: incompatible implicit declaration of built-in function ‘free’ [-Wbuiltin-declaration-mismatch] 155 | free(h+hmin); | ^~~~ mott_api.c:155:5: note: include ‘’ or provide a declaration of ‘free’ mott_api.c: In function ‘GetHistogram’: mott_api.c:179:16: warning: implicit declaration of function ‘calloc’ [-Wimplicit-function-declaration] 179 | h = (double*)calloc(*hmax-*hmin+1,sizeof(double))-*hmin; | ^~~~~~ mott_api.c:179:16: note: include ‘’ or provide a declaration of ‘calloc’ mott_api.c:179:16: warning: incompatible implicit declaration of built-in function ‘calloc’ [-Wbuiltin-declaration-mismatch] mott_api.c:179:16: note: include ‘’ or provide a declaration of ‘calloc’ mott_api.c: In function ‘PseudoResidueFrequencies2’: mott_api.c:207:12: warning: implicit declaration of function ‘toupper’ [-Wimplicit-function-declaration] 207 | freq[toupper(seq[n])]++; | ^~~~~~~ mott_api.c:5:1: note: include ‘’ or provide a declaration of ‘toupper’ 4 | #include"gapstat.h" +++ |+#include 5 | mott_api.c: In function ‘RobinsonResidueFrequencies2’: mott_api.c:230:27: warning: incompatible implicit declaration of built-in function ‘calloc’ [-Wbuiltin-declaration-mismatch] 230 | double *freq = (double*)calloc(256, sizeof(double)); | ^~~~~~ mott_api.c:230:27: note: include ‘’ or provide a declaration of ‘calloc’ aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gaplib.o gaplib.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../../dynlibsrc -I../../base wise2_mott_bridge.c ar ru libmott.a mott_api.o gaplib.o wise2_mott_bridge.o ar: `u' modifier ignored since `D' is the default (see `U') 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 '/<>/src/external/mott' make[3]: Leaving directory '/<>/src/external' (cd socket ; make CC="aarch64-linux-gnu-gcc" CFLAGS="-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c `aarch64-linux-gnu-pkg-config --cflags glib-2.0`" libwisesocket.a ) make[3]: Entering directory '/<>/src/socket' aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ functionserver.c functionserver.dy: In function ‘Wise2_main_loop_forking_FunctionServer’: functionserver.dy:129:11: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 129 | write(new_socket,buf,9); | ^~~~~~~~~~~~~~~~~~~~~~~ functionserver.dy:141:9: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 141 | write(new_socket,buf,6); | ^~~~~~~~~~~~~~~~~~~~~~~ functionserver.dy:183:9: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 183 | write(new_socket,buf,5); | ^~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ functionclient.c functionclient.dy: In function ‘Wise2_new_FunctionProxyCoordinator’: functionclient.dy:193:24: warning: passing argument 2 of ‘connect’ from incompatible pointer type [-Wincompatible-pointer-types] 193 | connect(out->socket, &server, sizeof(server)); | ^~~~~~~ | | | struct sockaddr_in * In file included from functionclient.c:7: /usr/aarch64-linux-gnu/include/sys/socket.h:126:52: note: expected ‘const struct sockaddr *’ but argument is of type ‘struct sockaddr_in *’ 126 | extern int connect (int __fd, __CONST_SOCKADDR_ARG __addr, socklen_t __len); | ^ aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ anonobj.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ transferinterface.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ directsocketwrite.c ar ru libwisesocket.a functionserver.o functionclient.o anonobj.o transferinterface.o directsocketwrite.o ar: `u' modifier ignored since `D' is the default (see `U') 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 '/<>/src/socket' (cd dnaindex ; make CC="aarch64-linux-gnu-gcc" CFLAGS="-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c `aarch64-linux-gnu-pkg-config --cflags glib-2.0`" all ) make[3]: Entering directory '/<>/src/dnaindex' aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly.c kmer_assembly.dy: In function ‘Wise2_show_KmerAssemblyNode’: kmer_assembly.dy:296:15: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 296 | fprintf(ofp,"Node %ld of sequence %s \n",node->number,buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly.dy:302:17: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 302 | fprintf(ofp," ... prev ... %c, %d to %ld\n",node->prev[i]->base,node->prev[i]->sequence_label_len,node->prev[i]->prev->number); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly.dy:309:17: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 309 | fprintf(ofp," ... next ... %c, %d to %ld\n",node->next[i]->base,node->next[i]->sequence_label_len,node->next[i]->next->number); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly.dy: In function ‘Wise2_remove_sequence_label_KmerAssemblyLink’: kmer_assembly.dy:365:18: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘KmerAssemblyLink *’ [-Wformat=] 365 | fprintf(stderr," ...unable to remove label %ld from link %ld (%d labels)\n",label,kal,kal->sequence_label_len); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ | | | KmerAssemblyLink * kmer_assembly.dy:367:20: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=] 367 | fprintf(stderr," [%ld] is %d label\n",kal->sequence_label[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_index_interface.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_direct.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_hash.c kmer_hash.dy: In function ‘Wise2_free_KmerHashIndex’: kmer_hash.dy:318:19: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 318 | fprintf(stderr, "min_kmer: %016lx\n", khi->min_kmer); | ^~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_hash.dy:319:19: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 319 | fprintf(stderr, "max_kmer: %016lx\n", khi->max_kmer); | ^~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ | | | kmer_t {aka long long int} aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_count.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_glib_index.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models singleseqspace.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models dnamapping.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models largeseqreader.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_untangler.c kmer_assembly_untangler.dy: In function ‘Wise2_show_KmerAssemblyPath’: kmer_assembly_untangler.dy:52:65: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 52 | fprintf(ofp,"%3d memory %d, from [%s] to [%s], base %c\n",i,(int)kap->stack[i],back,forw,kap->stack[i]->base); | ^ kmer_assembly_untangler.dy: In function ‘Wise2_untangle_KmerAssembly’: kmer_assembly_untangler.dy:120:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 120 | fprintf(stderr,"TANGLE: Node %ld, %s has forward %d and back %d links\n",node->number,buffer,node->next_len,node->prev_len); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:141:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 141 | fprintf(stderr,"Will attempt untangle starting at %ld to %ld\n",node->prev[i]->prev->number,node->number); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:141:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 141 | fprintf(stderr,"Will attempt untangle starting at %ld to %ld\n",node->prev[i]->prev->number,node->number); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:157:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 157 | fprintf(stderr,"RESOLVED: Node %ld [%s] Fully untangled now...\n",node->number,buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:159:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 159 | fprintf(stderr,"UNRESOLVED: Node %ld [%s] still tangled...\n",node->number,buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy: In function ‘Wise2_old_attempt_forward_untangle_KmerAssembly’: kmer_assembly_untangler.dy:444:20: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 444 | fprintf(stderr,"looking at node %ld with path length %d, next length %d depth %d\n",current->next->number,pathlen,current->next->next_len,current->sequence_label_len); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:568:82: warning: passing argument 4 of ‘Wise2_lift_backward_tangled_tail’ from incompatible pointer type [-Wincompatible-pointer-types] 568 | lift_backward_tangled_tail(kai,newpath->stack[newpath->stack_len-1],path,transferred_label,transferred_pos,transferred_len); | ^~~~~~~~~~~~~~~~~ | | | long int * In file included from kmer_assembly_untangler.c:4: kmer_assembly_untangler.h:174:116: note: expected ‘int *’ but argument is of type ‘long int *’ 174 | void Wise2_lift_backward_tangled_tail(KmerAssemblyIndex * kai,KmerAssemblyLink * new,KmerAssemblyPath * tail,int * start_label,SinglePosSequence ** positions,int label_len); | ~~~~~~^~~~~~~~~~~ kmer_assembly_untangler.dy: In function ‘Wise2_lift_forward_tangled_KmerAssemblyPath’: kmer_assembly_untangler.dy:746:20: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 6 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 746 | fprintf(stderr,"Moving stack position %d, depth %d, transfer %d, between %ld [%s] and %ld [%s]\n",i,kap->stack[i]->sequence_label_len,label_len,kap->stack[i]->prev->number,back,kap->stack[i]->next->number,forw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_untangler.dy:746:20: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 8 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 746 | fprintf(stderr,"Moving stack position %d, depth %d, transfer %d, between %ld [%s] and %ld [%s]\n",i,kap->stack[i]->sequence_label_len,label_len,kap->stack[i]->prev->number,back,kap->stack[i]->next->number,forw); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | kmer_t {aka long long int} aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_contig.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_error.c kmer_assembly_error.dy: In function ‘Wise2_mark_tangles_KmerAssembly’: kmer_assembly_error.dy:93:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 93 | fprintf(stderr,"Marking node (%ld) [%s] as next tangled\n",node->number,buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_error.dy:105:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 105 | fprintf(stderr,"Marking node (%ld) [%s] as prev tangled\n",node->number,buffer); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | kmer_t {aka long long int} kmer_assembly_error.dy: In function ‘Wise2_extend_indel_path_KmerAssembly’: kmer_assembly_error.dy:351:24: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int *’ [-Wformat=] 351 | fprintf(stderr,"in considering indel (%d, path %d), real (%c) and error (%c) do not agree at position %d,%d\n",delete_length,current_path,real->base,error->base,real_pos,error_pos); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~ | | | int * aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models compressed_protein_index.c compressed_protein_index.dy: In function ‘Wise2_add_direct_number_CompressedProteinIndex’: compressed_protein_index.dy:223:10: warning: returning ‘void *’ from a function with return type ‘boolean’ {aka ‘int’} makes integer from pointer without a cast [-Wint-conversion] 223 | return NULL; | ^~~~ make[3]: Leaving directory '/<>/src/dnaindex' (cd network ; make CC="aarch64-linux-gnu-gcc" CFLAGS="-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c `aarch64-linux-gnu-pkg-config --cflags glib-2.0`" all ) make[3]: Entering directory '/<>/src/network' aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex wise_proteinindex_server.c wise_proteinindex_server.c: In function ‘show_version’: wise_proteinindex_server.c:28:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 28 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex net_hspscan.c aarch64-linux-gnu-gcc -g -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -ldyna_glib -ldyna -lwisesocket -lwisebase -Wl,-z,relro -Wl,-z,now -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `aarch64-linux-gnu-pkg-config --libs glib-2.0` -lpthread aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex client_multihspscan.c make[3]: Leaving directory '/<>/src/network' (cd models ; make CC="aarch64-linux-gnu-gcc" CFLAGS="-g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c `aarch64-linux-gnu-pkg-config --cflags glib-2.0`" EXTRALIBS="-lm" HMMER_DEFINE="HMMER_INTERNAL" HMMER_INCLUDE="../HMMer2/" HMMER_LIBS="../HMMer2/" all ) make[3]: Entering directory '/<>/src/models' aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dnal.c dnal.c: In function ‘show_version’: dnal.c:106:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 106 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dnaalign.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ seqaligndisplay.c aarch64-linux-gnu-gcc -o dnal dnal.o dnaalign.o seqaligndisplay.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ psw.c psw.c: In function ‘show_version’: psw.c:261:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 261 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ proteinsw.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ sw_wrap.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ abc.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pba.c aarch64-linux-gnu-gcc -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pswdb.c pswdb.c: In function ‘show_version’: pswdb.c:97:106: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 97 | fprintf(stdout,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ aarch64-linux-gnu-gcc -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dbac.c dbac.c: In function ‘show_version’: dbac.c:364:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 364 | fprintf(ofp," Compiled %s\n",COMPILE_DATE); | ^~~~~~~~~~~~ dbac.c: In function ‘make_SeqAlign_from_align’: dbac.c:413:32: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 413 | fprintf(stderr,"Got %d with %d vs %d\n",i,strlen(seq),one->len); | ~^ ~~~~~~~~~~~ | | | | int size_t {aka long unsigned int} | %ld aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dba.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ slimdba.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ bigdba.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dbadisplay.c aarch64-linux-gnu-gcc -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include estwise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. estwise.c: In function ‘show_version’: estwise.c:559:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 559 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparser21.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparameter.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genestats.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisehsp.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneutil.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneoutput.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ threestatemodel.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genefrequency.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ splicesitemodeler.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise4.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise6.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genestretch6.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise21.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneloop21.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneloop6.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genephase6.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ gwlite.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ gwlitemodel.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ gwrap.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ matchsum.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estwrap.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisemodel.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ phasemodel.c phasemodel.dy: In function ‘Wise2_read_fasta_PhasedProtein’: phasemodel.dy:241:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fgets(name,10000,ifp); | ^~~~~~~~~~~~~~~~~~~~~ phasemodel.dy:241:3: warning: ‘fgets’ writing 10000 bytes into a region of size 2000 overflows the destination [-Wstringop-overflow=] 241 | fgets(name,10000,ifp); | ^~~~~~~~~~~~~~~~~~~~~ phasemodel.dy:235:8: note: destination object ‘name’ of size 2000 235 | char name[2000]; | ^~~~ In file included from /usr/aarch64-linux-gnu/include/stdio.h:906, from ../base/wisebase.h:6, from ../dynlibsrc/probability.h:7, from geneparser21.h:6, from genewisemodel.h:6, from phasemodel.h:6, from phasemodel.c:4: /usr/aarch64-linux-gnu/include/bits/stdio2.h:209:1: note: in a call to function ‘fgets’ declared with attribute ‘access (write_only, 1, 2)’ 209 | fgets (char *__restrict __s, int __n, FILE *__restrict __stream) | ^~~~~ In function ‘fgets’, inlined from ‘Wise2_read_fasta_PhasedProtein’ at phasemodel.dy:241:3: /usr/aarch64-linux-gnu/include/bits/stdio2.h:215:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 215 | return __fgets_chk_warn (__s, sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ cdparser.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genedisplay.c genedisplay.dy: In function ‘Wise2_write_intron_desc’: genedisplay.dy:493:20: warning: too many arguments for format [-Wformat-extra-args] 493 | sprintf(buffer," Intron ??? ",in_number); | ^~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estwise3.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estslim3.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estloop3.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estfrag3.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estslimloop.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ gwquickdb.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ threestatedb.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pfamhmmer1db.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pwmdna.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../HMMer2/ -DHMMER_INTERNAL -I../base/ -I../dynlibsrc/ wise2xhmmer2.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisemodeldb.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ seqhit.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ standardout.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparser4.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estquick3.c aarch64-linux-gnu-gcc -g -o estwise estwise.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0` aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include genewise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. genewise.c: In function ‘show_version’: genewise.c:860:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 860 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ aarch64-linux-gnu-gcc -o genewise genewise.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase -lm -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0` aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include genewisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ genewisedb.c: In function ‘show_version’: genewisedb.c:1005:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 1005 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ aarch64-linux-gnu-gcc -g -o genewisedb genewisedb.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0` aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include estwisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ estwisedb.c: In function ‘show_version’: estwisedb.c:838:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 838 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ aarch64-linux-gnu-gcc -g -o estwisedb estwisedb.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0` aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genomewise.c genomewise.c: In function ‘show_version’: genomewise.c:18:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 18 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genomewise9.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genome_evidence.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ est_evidence.c est_evidence.dy: In function ‘Wise2_new_est_GenomeEvidenceUnit’: est_evidence.dy:142:16: warning: assignment to ‘int (*)(void *)’ from incompatible pointer type ‘Wise2_EstEvidence * (*)(Wise2_EstEvidence *)’ [-Wincompatible-pointer-types] 142 | in->geu_free = free_EstEvidence; | ^ aarch64-linux-gnu-gcc -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ sywise.c sywise.c: In function ‘show_version’: sywise.c:14:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 14 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ sywise20.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ syexonmodel.c aarch64-linux-gnu-gcc -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pseudowise.c pseudowise.c: In function ‘show_version’: pseudowise.c:15:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 15 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pseudowise7.c aarch64-linux-gnu-gcc -g -o pseudowise pseudowise.o pseudowise7.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase -lm -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0` aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ `aarch64-linux-gnu-pkg-config --cflags glib-2.0` promoterwise.c promoterwise.c: In function ‘show_version’: promoterwise.c:17:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 17 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ localdba.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ `aarch64-linux-gnu-pkg-config --cflags glib-2.0` localcishit.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ localcispara.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ motifmatrix.c motifmatrix.c: In function ‘Wise2_MotifConsMatrix_alloc_matrix’: motifmatrix.c:408:24: warning: assignment to ‘char’ from ‘void *’ makes integer from pointer without a cast [-Wint-conversion] 408 | for(i=0;i>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ motifmatrixdp.c aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ transfactor.c transfactor.dy: In function ‘Wise2_read_ben_IUPAC_TransFactorSet’: transfactor.dy:680:21: warning: ‘%s’ directive writing up to 511 bytes into a region of size between 495 and 504 [-Wformat-overflow=] 680 | sprintf(sbuffer,"motif_%d_%s",motif_no,buffer); | ^~~~~~~~~~~~~ ~~~~~~ In file included from /usr/aarch64-linux-gnu/include/stdio.h:906, from ../base/wisebase.h:6, from pwmdna.h:6, from transfactor.h:6, from transfactor.c:4: In function ‘sprintf’, inlined from ‘Wise2_read_ben_IUPAC_TransFactorSet’ at transfactor.dy:680:5: /usr/aarch64-linux-gnu/include/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 9 and 529 bytes into a destination of size 512 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pairwiseshortdna.c aarch64-linux-gnu-gcc -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm `aarch64-linux-gnu-pkg-config --libs glib-2.0` -lpthread aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c scanwisep.c: In function ‘show_version’: scanwisep.c:423:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 423 | fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); | ^~~~~~~~~~~~ aarch64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ `aarch64-linux-gnu-pkg-config --cflags glib-2.0` hsp2aln_sw.c aarch64-linux-gnu-gcc -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 -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0` -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase -lm -lpthread -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-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: `u' modifier ignored since `D' is the default (see `U') ar: creating libmodel.a make[3]: Leaving directory '/<>/src/models' make bin make[3]: Entering directory '/<>/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 /<>/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 '/<>/src' make[2]: Leaving directory '/<>/src' /usr/bin/make -C debian/manpages.d make[2]: Entering directory '/<>/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 '/<>/debian/manpages.d' find src/models/ src/dynlibsrc/ -name '*.tex' -print0 | LC_ALL=C sort -z | xargs -0 cat | 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 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./api.tex LaTeX2e <2023-11-01> L3 programming layer <2023-11-09> (/usr/share/texlive/texmf-dist/tex/latex/base/latex209.def Entering LaTeX 2.09 COMPATIBILITY MODE ************************************************************* !!WARNING!! !!WARNING!! !!WARNING!! !!WARNING!! This mode attempts to provide an emulation of the LaTeX 2.09 author environment so that OLD documents can be successfully processed. It should NOT be used for NEW documents! New documents should use Standard LaTeX conventions and start with the \documentclass command. Compatibility mode is UNLIKELY TO WORK with LaTeX 2.09 style files that change any internal macros, especially not with those that change the FONT SELECTION or OUTPUT ROUTINES. Therefore such style files MUST BE UPDATED to use Current Standard LaTeX: LaTeX2e. If you suspect that you may be using such a style file, which is probably very, very old by now, then you should attempt to get it updated by sending a copy of this error message to the author of that file. ************************************************************* (/usr/share/texlive/texmf-dist/tex/latex/base/tracefnt.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/latexsym.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2023/05/17 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) No file api.aux. (/usr/share/texlive/texmf-dist/tex/latex/base/ulasy.fd) [1{/var/lib/texmf/fonts /map/pdftex/updmap/pdftex.map}] No file api.toc. [2] [3] Overfull \hbox (1.49698pt too wide) in paragraph at lines 109--109 [] \OT1/cmtt/m/n/10 print "You must give a file to revcom for a reverse to w ork!";[] [4] [5] LaTeX Warning: Reference `object_CodonTable' on page 6 undefined on input line 198. LaTeX Warning: Reference `object_Sequence' on page 6 undefined on input line 19 9. LaTeX Warning: Reference `object_CompMat' on page 6 undefined on input line 205 . LaTeX Warning: Reference `object_Sequence' on page 6 undefined on input line 20 6. LaTeX Warning: Reference `object_Protein' on page 6 undefined on input line 207 . LaTeX Warning: Reference `object_CompMat' on page 6 undefined on input line 208 . LaTeX Warning: Reference `module_sw_wrap' on page 6 undefined on input line 209 . LaTeX Warning: Reference `module_seqaligndisplay' on page 6 undefined on input line 210. LaTeX Warning: Reference `object_Protein' on page 6 undefined on input line 215 . LaTeX Warning: Reference `object_Sequence' on page 6 undefined on input line 21 5. [6] LaTeX Warning: Reference `object_ProteinDB' on page 7 undefined on input line 2 16. LaTeX Warning: Reference `object_ProteinDB' on page 7 undefined on input line 2 17. LaTeX Warning: Reference `module_sw_wrap' on page 7 undefined on input line 218 . LaTeX Warning: Reference `object_Hscore' on page 7 undefined on input line 219. LaTeX Warning: Reference `object_DataEntry' on page 7 undefined on input line 2 21. LaTeX Warning: Reference `object_ProteinDB' on page 7 undefined on input line 2 21. LaTeX Warning: Reference `object_Sequence' on page 7 undefined on input line 22 8. LaTeX Warning: Reference `object_Protein' on page 7 undefined on input line 229 . LaTeX Warning: Reference `object_Sequence' on page 7 undefined on input line 23 0. LaTeX Warning: Reference `object_Genomic' on page 7 undefined on input line 231 . LaTeX Warning: Reference `object_GeneFrequency' on page 7 undefined on input li ne 233. LaTeX Warning: Reference `object_CodonTable' on page 7 undefined on input line 234. LaTeX Warning: Reference `object_RandomModelDNA' on page 7 undefined on input l ine 235. 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. Overfull \hbox (21.30891pt too wide) in paragraph at lines 237--238 []\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 238. LaTeX Warning: Reference `module_gwrap' on page 7 undefined on input line 239. [7] [8] [9] LaTeX Warning: Reference `module_gwrap' on page 10 undefined on input line 389. [10] LaTeX Warning: Reference `module_estwrap' on page 11 undefined on input line 39 1. LaTeX Warning: Reference `module_sw_wrap' on page 11 undefined on input line 39 3. LaTeX Warning: Reference `module_genedisplay' on page 11 undefined on input lin e 395. LaTeX Warning: Reference `module_seqaligndisplay' on page 11 undefined on input line 397. LaTeX Warning: Reference `module_threestatemodel' on page 11 undefined on input line 399. LaTeX Warning: Reference `module_threestatedb' on page 11 undefined on input li ne 400. LaTeX Warning: Reference `module_genefrequency' on page 11 undefined on input l ine 401. LaTeX Warning: Reference `module_geneparameter' on page 11 undefined on input l ine 402. LaTeX Warning: Reference `module_cdparser' on page 11 undefined on input line 4 03. LaTeX Warning: Reference `module_sequence' on page 11 undefined on input line 4 10. LaTeX Warning: Reference `module_sequencedb' on page 11 undefined on input line 411. LaTeX Warning: Reference `module_protein' on page 11 undefined on input line 41 2. LaTeX Warning: Reference `module_proteindb' on page 11 undefined on input line 413. LaTeX Warning: Reference `module_genomic' on page 11 undefined on input line 41 4. LaTeX Warning: Reference `module_genomicdb' on page 11 undefined on input line 415. LaTeX Warning: Reference `module_cdna' on page 11 undefined on input line 416. LaTeX Warning: Reference `module_cdnadb' on page 11 undefined on input line 417 . LaTeX Warning: Reference `module_probability' on page 11 undefined on input lin e 423. LaTeX Warning: Reference `module_codon' on page 11 undefined on input line 424. LaTeX Warning: Reference `module_compmat' on page 11 undefined on input line 42 5. LaTeX Warning: Reference `module_codonmat' on page 11 undefined on input line 4 26. LaTeX Warning: Reference `module_codonmapper' on page 11 undefined on input lin e 427. [11] LaTeX Warning: Reference `module_hscore' on page 12 undefined on input line 433 . LaTeX Warning: Reference `module_histogram' on page 12 undefined on input line 434. LaTeX Warning: Reference `module_dbimpl' on page 12 undefined on input line 435 . LaTeX Warning: Reference `module_aln' on page 12 undefined on input line 441. LaTeX Warning: Reference `module_packaln' on page 12 undefined on input line 44 2. LaTeX Warning: Reference `module_basematrix' on page 12 undefined on input line 443. LaTeX Warning: Reference `object_AlnBlock' on page 12 undefined on input line 4 51. LaTeX Warning: Reference `object_AlnColumn' on page 12 undefined on input line 453. LaTeX Warning: Reference `object_AlnUnit' on page 12 undefined on input line 45 5. LaTeX Warning: Reference `object_AlnSequence' on page 12 undefined on input lin e 457. LaTeX Warning: Reference `accessing_fields' on page 12 undefined on input line 464. Overfull \hbox (6.8248pt too wide) in paragraph at lines 475--482 \OT1/cmr/m/n/10 AlnBlock is the main rep-re-sen-ta-tion of align-ments from Dy- na-mite. Each AlnBlock [12] (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) LaTeX Warning: Reference `accessing_fields' on page 13 undefined on input line 513. [13] LaTeX Warning: Reference `accessing_fields' on page 14 undefined on input line 555. [14] LaTeX Warning: Reference `accessing_fields' on page 15 undefined on input line 623. [15] LaTeX Warning: Reference `object_AlnRange' on page 16 undefined on input line 6 52. LaTeX Warning: Reference `object_AlnRangeSet' on page 16 undefined on input lin e 654. LaTeX Warning: Reference `accessing_fields' on page 16 undefined on input line 661. LaTeX Warning: Reference `accessing_fields' on page 16 undefined on input line 688. [16] LaTeX Warning: Reference `object_cDNA' on page 17 undefined on input line 741. LaTeX Warning: Reference `accessing_fields' on page 17 undefined on input line 748. [17] [18] [19] LaTeX Warning: Reference `object_cDNADB' on page 20 undefined on input line 884 . LaTeX Warning: Reference `accessing_fields' on page 20 undefined on input line 924. [20] LaTeX Warning: Reference `object_CodonTable' on page 21 undefined on input line 1005. [21] [22] [23] [24] LaTeX Warning: Reference `accessing_fields' on page 25 undefined on input line 1213. [25] [26] [27] LaTeX Warning: Reference `object_CodonMapper' on page 28 undefined on input lin e 1363. LaTeX Warning: Reference `accessing_fields' on page 28 undefined on input line 1391. [28] Overfull \hbox (12.33003pt too wide) in paragraph at lines 1418--1419 []\OT1/cmtt/m/n/10 &Wise2::CodonMapper::sprinkle[]errors[]over[]CodonMapper (cm ,error) LaTeX Warning: Reference `object_ComplexSequence' on page 29 undefined on input line 1442. LaTeX Warning: Reference `object_ComplexSequenceEvalSet' on page 29 undefined o n input line 1444. LaTeX Warning: Reference `accessing_fields' on page 29 undefined on input line 1451. [29] LaTeX Warning: Reference `accessing_fields' on page 30 undefined on input line 1482. LaTeX Warning: Reference `object_CompMat' on page 30 undefined on input line 15 17. LaTeX Warning: Reference `accessing_fields' on page 30 undefined on input line 1524. [30] [31] LaTeX Warning: Reference `object_DBSearchImpl' on page 32 undefined on input li ne 1624. [32] LaTeX Warning: Reference `accessing_fields' on page 33 undefined on input line 1671. [33] LaTeX Warning: Reference `object_DnaMatrix' on page 34 undefined on input line 1736. LaTeX Warning: Reference `object_DnaProbMatrix' on page 34 undefined on input l ine 1738. [34] LaTeX Warning: Reference `accessing_fields' on page 35 undefined on input line 1799. LaTeX Warning: Reference `accessing_fields' on page 35 undefined on input line 1812. [35] LaTeX Warning: Reference `object_Gene' on page 36 undefined on input line 1844. LaTeX Warning: Reference `accessing_fields' on page 36 undefined on input line 1851. [36] [37] LaTeX Warning: Reference `object_Genomic' on page 38 undefined on input line 19 48. LaTeX Warning: Reference `object_GenomicRepeat' on page 38 undefined on input l ine 1950. [38] Overfull \hbox (0.5938pt too wide) in paragraph at lines 1989--1990 []\OT1/cmtt/m/n/10 Wise2[]Genomic[]from[]Sequence[]Nheuristic (seq,length[]of[] N) LaTeX Warning: Reference `accessing_fields' on page 39 undefined on input line 2038. [39] [40] LaTeX Warning: Reference `accessing_fields' on page 41 undefined on input line 2150. [41] LaTeX Warning: Reference `object_GenomicDB' on page 42 undefined on input line 2168. Overfull \hbox (65.9032pt too wide) in paragraph at lines 2175--2176 []\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 2176--2177 []\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 2192--2193 []\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 2193--2194 []\OT1/cmtt/m/n/10 &Wise2::new[]GenomicDB (seqdb,cses,length[]of[]N,repeat[]in[ ]cds[]score) [42] LaTeX Warning: Reference `accessing_fields' on page 43 undefined on input line 2213. [43] LaTeX Warning: Reference `object_GenomicRegion' on page 44 undefined on input l ine 2298. LaTeX Warning: Reference `accessing_fields' on page 44 undefined on input line 2305. [44] Overfull \hbox (1.83012pt too wide) in paragraph at lines 2348--2349 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::read[]EMBL[]GenomicRegion[]file (file name) [45] Overfull \hbox (7.08008pt too wide) in paragraph at lines 2401--2402 []\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 2426--2427 []\OT1/cmtt/m/n/10 Wise2[]show[]pretty[]GenomicRegion (gr,show[]supporting,ofp) Overfull \hbox (59.57962pt too wide) in paragraph at lines 2427--2428 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::show[]pretty[]GenomicRegion (gr,show[ ]supporting,ofp) [46] [47] LaTeX Warning: Reference `object_Histogram' on page 48 undefined on input line 2505. [48] LaTeX Warning: Reference `accessing_fields' on page 49 undefined on input line 2553. Overfull \hbox (32.9967pt too wide) in paragraph at lines 2592--2592 [] \OT1/cmtt/m/n/10 b) cooperation with future versions of histogram.c would be possible.[] [49] [50] [51] Overfull \hbox (123.4428pt too wide) in paragraph at lines 2794--2795 []\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 2795--2796 []\OT1/cmtt/m/n/10 &Wise2::Histogram::set[]EVD (h,mu,lambda,lowbound,highbound, wonka,ndegrees) Overfull \hbox (33.66461pt too wide) in paragraph at lines 2797--2798 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->set[]EVD(mu,lambda,lowbound,highbound ,wonka,ndegrees) [52] [53] [54] LaTeX Warning: Reference `object_Hscore' on page 55 undefined on input line 293 0. LaTeX Warning: Reference `object_DataScore' on page 55 undefined on input line 2932. LaTeX Warning: Reference `object_DataEntry' on page 55 undefined on input line 2934. LaTeX Warning: Reference `accessing_fields' on page 55 undefined on input line 2961. Overfull \hbox (30.97293pt too wide) in paragraph at lines 2971--2972 []\OT1/cmr/m/n/10 should[]store Type [boolean (*should[]store)(int given[]score ,double in-ter-nal[]score[]level) [55] [56] [57] LaTeX Warning: Reference `accessing_fields' on page 58 undefined on input line 3162. [58] LaTeX Warning: Reference `accessing_fields' on page 59 undefined on input line 3188. LaTeX Warning: Reference `object_PackAln' on page 59 undefined on input line 32 29. [59] LaTeX Warning: Reference `object_PackAlnUnit' on page 60 undefined on input lin e 3231. LaTeX Warning: Reference `accessing_fields' on page 60 undefined on input line 3238. [60] LaTeX Warning: Reference `accessing_fields' on page 61 undefined on input line 3308. [61] [62] LaTeX Warning: Reference `object_Protein' on page 63 undefined on input line 34 31. LaTeX Warning: Reference `accessing_fields' on page 63 undefined on input line 3438. [63] LaTeX Warning: Reference `object_ProteinDB' on page 64 undefined on input line 3488. LaTeX Warning: Reference `accessing_fields' on page 64 undefined on input line 3545. [64] LaTeX Warning: Reference `object_RandomProteinDB' on page 65 undefined on input line 3590. LaTeX Warning: Reference `object_RandomDNADB' on page 65 undefined on input lin e 3592. LaTeX Warning: Reference `accessing_fields' on page 65 undefined on input line 3599. LaTeX Warning: Reference `accessing_fields' on page 65 undefined on input line 3620. [65] LaTeX Warning: Reference `object_RandomModelDNA' on page 66 undefined on input line 3642. LaTeX Warning: Reference `object_RandomModel' on page 66 undefined on input lin e 3644. LaTeX Warning: Reference `accessing_fields' on page 66 undefined on input line 3682. [66] LaTeX Warning: Reference `accessing_fields' on page 67 undefined on input line 3697. LaTeX Warning: Reference `object_Sequence' on page 67 undefined on input line 3 713. LaTeX Warning: Reference `object_SequenceSet' on page 67 undefined on input lin e 3715. [67] LaTeX Warning: Reference `accessing_fields' on page 68 undefined on input line 3779. [68] Overfull \hbox (16.34366pt too wide) in paragraph at lines 3839--3840 []\OT1/cmtt/m/n/10 Wise2[]force[]to[]dna[]Sequence (seq,fraction,number[]of[]co nver) [69] [70] [71] [72] [73] [74] LaTeX Warning: Reference `accessing_fields' on page 75 undefined on input line 4176. [75] [76] LaTeX Warning: Reference `object_SequenceDB' on page 77 undefined on input line 4265. LaTeX Warning: Reference `object_FileSource' on page 77 undefined on input line 4267. LaTeX Warning: Reference `accessing_fields' on page 77 undefined on input line 4294. [77] LaTeX Warning: Reference `accessing_fields' on page 78 undefined on input line 4355. LaTeX Warning: Reference `object_Exon' on page 78 undefined on input line 4381. LaTeX Warning: Reference `object_Transcript' on page 78 undefined on input line 4383. [78] LaTeX Warning: Reference `accessing_fields' on page 79 undefined on input line 4390. LaTeX Warning: Reference `accessing_fields' on page 79 undefined on input line 4413. [79] LaTeX Warning: Reference `object_Translation' on page 80 undefined on input lin e 4482. LaTeX Warning: Reference `accessing_fields' on page 80 undefined on input line 4489. Overfull \hbox (24.01358pt too wide) in paragraph at lines 4508--4515 \OT1/cmr/m/n/10 have any se-quence in it. When se-quence is asked for by get[]P rotein[]from[]Translation() [80] LaTeX Warning: Reference `object_cDNAParser' on page 81 undefined on input line 4549. [81] LaTeX Warning: Reference `accessing_fields' on page 82 undefined on input line 4579. LaTeX Warning: Reference `object_DnaStartEnd' on page 82 undefined on input lin e 4602. Overfull \hbox (62.7533pt too wide) in paragraph at lines 4609--4610 []\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 4610--4611 []\OT1/cmtt/m/n/10 &Wise2::make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap ,text,dpri) [82] LaTeX Warning: Reference `accessing_fields' on page 83 undefined on input line 4655. Overfull \hbox (335.96082pt too wide) in paragraph at lines 4671--4672 []\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 4672--4673 []\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) [83] Overfull \hbox (329.87091pt too wide) in paragraph at lines 4698--4699 []\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 4699--4700 []\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) [84] Overfull \hbox (265.40146pt too wide) in paragraph at lines 4732--4733 []\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 4733--4734 []\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) [85] Overfull \hbox (47.00343pt too wide) in paragraph at lines 4780--4781 []\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 4781--4782 []\OT1/cmtt/m/n/10 &Wise2::protein2genomic[]ascii[]display (alb,p,gen,ct,name,m ain,ofp) [86] Overfull \hbox (188.7522pt too wide) in paragraph at lines 4801--4802 []\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 4802--4803 []\OT1/cmtt/m/n/10 &Wise2::protcdna[]ascii[]display (alb,protsequence,protname, protoff,cdna,ct,name,main,mult,ofp) LaTeX Warning: Reference `object_GeneFrequency21' on page 87 undefined on input line 4830. LaTeX Warning: Reference `object_GeneConsensus' on page 87 undefined on input l ine 4832. LaTeX Warning: Reference `object_GeneSingleCons' on page 87 undefined on input line 4834. [87] LaTeX Warning: Reference `accessing_fields' on page 88 undefined on input line 4879. Overfull \hbox (1.40793pt too wide) in paragraph at lines 4893--4894 []\OT1/cmr/m/n/10 transition[GENEFREQUENCY21[]TRANSITION[]LEN] Type [dou-ble : Scalar] LaTeX Warning: Reference `accessing_fields' on page 88 undefined on input line 4906. [88] LaTeX Warning: Reference `accessing_fields' on page 89 undefined on input line 4921. LaTeX Warning: Reference `object_GeneParameter21' on page 89 undefined on input line 4937. LaTeX Warning: Reference `accessing_fields' on page 89 undefined on input line 4944. [89] LaTeX Warning: Reference `object_MatchSummarySet' on page 90 undefined on input line 4990. LaTeX Warning: Reference `object_MatchSummary' on page 90 undefined on input li ne 4992. LaTeX Warning: Reference `accessing_fields' on page 90 undefined on input line 4999. Overfull \hbox (71.7832pt too wide) in paragraph at lines 5014--5015 []\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 5015--5016 []\OT1/cmtt/m/n/10 &Wise2::MatchSummarySet::MatchSummarySet[]from[]AlnBlock[]es twise Overfull \hbox (62.22433pt too wide) in paragraph at lines 5017--5018 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->MatchSummarySet[]from[]AlnBlock[]estw ise(qname,offset,target) [90] Overfull \hbox (82.28311pt too wide) in paragraph at lines 5040--5041 []\OT1/cmtt/m/n/10 Wise2[]MatchSummarySet[]from[]AlnBlock[]genewise (alb,qname, protoff,target) Overfull \hbox (7.08008pt too wide) in paragraph at lines 5041--5042 []\OT1/cmtt/m/n/10 &Wise2::MatchSummarySet::MatchSummarySet[]from[]AlnBlock[]ge newise Overfull \hbox (72.72424pt too wide) in paragraph at lines 5043--5044 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->MatchSummarySet[]from[]AlnBlock[]gene wise(qname,protoff,target) LaTeX Warning: Reference `accessing_fields' on page 91 undefined on input line 5065. [91] LaTeX Warning: Reference `object_PfamHmmer1DB' on page 92 undefined on input li ne 5107. LaTeX Warning: Reference `object_PfamHmmer1Entry' on page 92 undefined on input line 5109. LaTeX Warning: Reference `accessing_fields' on page 92 undefined on input line 5116. LaTeX Warning: Reference `accessing_fields' on page 92 undefined on input line 5152. [92] Overfull \hbox (92.78302pt too wide) in paragraph at lines 5174--5175 []\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 5175--5176 []\OT1/cmtt/m/n/10 &Wise2::write[]pretty[]str[]align (alb,qname,query,tname,tar get,name,main,ofp) [93] Overfull \hbox (3.5338pt too wide) in paragraph at lines 5217--5218 []\OT1/cmtt/m/n/10 Wise2[]write[]pretty[]Protein[]align (alb,q,t,name,main,ofp) LaTeX Warning: Reference `object_DnaSequenceHitList' on page 94 undefined on in put line 5243. LaTeX Warning: Reference `object_SegmentHitList' on page 94 undefined on input line 5245. LaTeX Warning: Reference `object_SegmentHit' on page 94 undefined on input line 5247. [94] LaTeX Warning: Reference `accessing_fields' on page 95 undefined on input line 5254. Overfull \hbox (29.5499pt too wide) in paragraph at lines 5290--5291 []\OT1/cmtt/m/n/10 &Wise2::DnaSequenceHitList::read[]MSPcrunch[]DnaSequenceHitL ist (ifp) [95] LaTeX Warning: Reference `accessing_fields' on page 96 undefined on input line 5307. LaTeX Warning: Reference `accessing_fields' on page 96 undefined on input line 5320. Overfull \hbox (99.50298pt too wide) in paragraph at lines 5348--5349 []\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 5349--5350 []\OT1/cmtt/m/n/10 &Wise2::Align[]strings[]ProteinSmithWaterman (one,two,comp,g ap,ext,dpenv,dpri) [96] Overfull \hbox (110.00288pt too wide) in paragraph at lines 5373--5374 []\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 5374--5375 []\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 5386--5387 []\OT1/cmr/m/n/10 [OWNER] new AlnBlock struc-ture rep-re-sent-ing the align-men t [AlnBlock [97] Overfull \hbox (68.00325pt too wide) in paragraph at lines 5407--5408 []\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 5408--5409 []\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 5434--5435 []\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]ABC (one,two,comp,a,b,c,dpenv,dpri) [98] Overfull \hbox (47.00343pt too wide) in paragraph at lines 5455--5456 []\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 5456--5457 []\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 5471--5474 \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 5478--5479 []\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 5479--5480 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinSW (querydb,targetdb,comp,gap,e xt,bits[]cutoff,report[]level,die[]on[]error,dbsi) [99] Overfull \hbox (235.37173pt too wide) in paragraph at lines 5500--5501 []\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 5501--5502 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b, c,bits[]cutoff,report[]level,die[]on[]error,dbsi) [100] Overfull \hbox (359.90063pt too wide) in paragraph at lines 5523--5524 []\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 5524--5525 []\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 101 undefined on input l ine 5552. LaTeX Warning: Reference `accessing_fields' on page 101 undefined on input line 5559. [101] Overfull \hbox (15.42177pt too wide) in paragraph at lines 5587--5588 []\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 5594--5595 []\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 5598--5599 []\OT1/cmr/m/n/10 index[]generic Type [Three-State-Model * (*in-dex[]generic)(T hreeStateDB *tdb,DataEntry [102] Overfull \hbox (29.5499pt too wide) in paragraph at lines 5669--5670 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateDB::new[]proteindb[]ThreeStateDB (sdb,comp ,gap,ext) [103] [104] LaTeX Warning: Reference `object_ThreeStateModel' on page 105 undefined on inpu t line 5732. LaTeX Warning: Reference `object_ThreeStateUnit' on page 105 undefined on input line 5734. LaTeX Warning: Reference `accessing_fields' on page 105 undefined on input line 5775. [105] Overfull \hbox (16.10999pt too wide) in paragraph at lines 5802--5803 []\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 5822--5823 []\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 5823--5824 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::force[]weighted[]local[]model (tsm, prob[]into[]model,ratio[]start,ratio[]end) Overfull \hbox (93.09401pt too wide) in paragraph at lines 5825--5826 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->force[]weighted[]local[]model(prob[]i nto[]model,ratio[]start,ratio[]end) Overfull \hbox (49.31339pt too wide) in paragraph at lines 5845--5846 []\OT1/cmtt/m/n/10 Wise2[]ThreeStateModel[]from[]half[]bit[]Sequence (pro,mat,r m,gap,ext) [106] Overfull \hbox (5.61008pt too wide) in paragraph at lines 5846--5847 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::ThreeStateModel[]from[]half[]bit[]S equence Overfull \hbox (39.75452pt too wide) in paragraph at lines 5848--5849 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->ThreeStateModel[]from[]half[]bit[]Seq uence(mat,rm,gap,ext) Overfull \hbox (51.38966pt too wide) in paragraph at lines 5872--5873 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::write[]HMMer[]1[]7[]ascii[]ThreeSta teModel (tsm,ofp) LaTeX Warning: Reference `accessing_fields' on page 107 undefined on input line 5890. [107] [108] (./api.aux) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tctt1000 mkdir: cannot create directory ‘././sbuild-nonexistent’: Permission denied mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tctt1000 This is METAFONT, Version 2.71828182 (TeX Live 2023/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tctt1000.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tctt.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf Ok [100] [109] [98] [99] [108]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrfract.mf Ok [188] [189] [190]) ) ) ) Font metrics written on tctt1000.tfm. Output written on tctt1000.600gf (128 characters, 19540 bytes). Transcript written on tctt1000.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/tctt1000.600pk: successfully generated. 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) kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tcrm1000 mkdir: cannot create directory ‘././sbuild-nonexistent’: Permission denied mktexpk: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1+0/600; nonstopmode; input tcrm1000 This is METAFONT, Version 2.71828182 (TeX Live 2023/Debian) (preloaded base=mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm1000.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exbase.mf) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/tcrm.mf (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymb.mf Ok (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/exaccess.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txpseudo.mf Ok) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txaccent.mf Ok [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [27] [29]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txgen.mf Ok [100] [109] [98] [99] [108]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txsymbol.mf Ok [13] [18] [21] [22] [23] [24] [25] [26] [28] [31] [32] [36] [39] [44] [45] [46] [42] [47] [60] [61] [62] [77] [79] [87] [110] [91] [93] [94] [95] [96] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] [159] [160] [161] [162] [163] [164] [165] [166] [167] [168] [169] [171] [172] [173] [174] [175] [177] [176] [180] [181] [182] [183] [184] [187] [191] [214] [246]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txromod.mf Ok [48] [49] [50] [51] [52] [53] [54] [55] [56] [57]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrsuper.mf Ok [185] [178] [179] [170] [186]) (/usr/share/texlive/texmf-dist/fonts/source/jknappen/ec/txrfract.mf Ok [188] [189] [190]) ) ) ) (some charht values had to be adjusted by as much as 0.06943pt) Font metrics written on tcrm1000.tfm. Output written on tcrm1000.600gf (128 characters, 23548 bytes). Transcript written on tcrm1000.log. mktexpk: /tmp/texfonts/pk/ljfour/jknappen/ec/tcrm1000.600pk: successfully generated. Output written on api.pdf (108 pages, 304185 bytes). Transcript written on api.log. cd docs && pdflatex api.tex This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./api.tex LaTeX2e <2023-11-01> L3 programming layer <2023-11-09> (/usr/share/texlive/texmf-dist/tex/latex/base/latex209.def Entering LaTeX 2.09 COMPATIBILITY MODE ************************************************************* !!WARNING!! !!WARNING!! !!WARNING!! !!WARNING!! This mode attempts to provide an emulation of the LaTeX 2.09 author environment so that OLD documents can be successfully processed. It should NOT be used for NEW documents! New documents should use Standard LaTeX conventions and start with the \documentclass command. Compatibility mode is UNLIKELY TO WORK with LaTeX 2.09 style files that change any internal macros, especially not with those that change the FONT SELECTION or OUTPUT ROUTINES. Therefore such style files MUST BE UPDATED to use Current Standard LaTeX: LaTeX2e. If you suspect that you may be using such a style file, which is probably very, very old by now, then you should attempt to get it updated by sending a copy of this error message to the author of that file. ************************************************************* (/usr/share/texlive/texmf-dist/tex/latex/base/tracefnt.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/latexsym.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2023/05/17 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./api.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ulasy.fd) [1{/var/lib /texmf/fonts/map/pdftex/updmap/pdftex.map}] (./api.toc [2] [3] [4] [5] [6] [7] [8] [9]) [10] [11] Overfull \hbox (1.49698pt too wide) in paragraph at lines 109--109 [] \OT1/cmtt/m/n/10 print "You must give a file to revcom for a reverse to w ork!";[] [12] [13] [14] LaTeX Warning: Reference `object_GeneFrequency' on page 15 undefined on input l ine 233. 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. Overfull \hbox (21.30891pt too wide) in paragraph at lines 237--238 []\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 238. LaTeX Warning: Reference `module_gwrap' on page 15 undefined on input line 239. [15] [16] [17] LaTeX Warning: Reference `module_gwrap' on page 18 undefined on input line 389. [18] LaTeX Warning: Reference `module_codonmat' on page 19 undefined on input line 4 26. [19] LaTeX Warning: Reference `module_dbimpl' on page 20 undefined on input line 435 . Overfull \hbox (6.8248pt too wide) in paragraph at lines 475--482 \OT1/cmr/m/n/10 AlnBlock is the main rep-re-sen-ta-tion of align-ments from Dy- na-mite. Each AlnBlock [20] (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] Overfull \hbox (12.33003pt too wide) in paragraph at lines 1418--1419 []\OT1/cmtt/m/n/10 &Wise2::CodonMapper::sprinkle[]errors[]over[]CodonMapper (cm ,error) [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] Overfull \hbox (0.5938pt too wide) in paragraph at lines 1989--1990 []\OT1/cmtt/m/n/10 Wise2[]Genomic[]from[]Sequence[]Nheuristic (seq,length[]of[] N) [47] [48] [49] Overfull \hbox (65.9032pt too wide) in paragraph at lines 2175--2176 []\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 2176--2177 []\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 2192--2193 []\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 2193--2194 []\OT1/cmtt/m/n/10 &Wise2::new[]GenomicDB (seqdb,cses,length[]of[]N,repeat[]in[ ]cds[]score) [50] [51] [52] Overfull \hbox (1.83012pt too wide) in paragraph at lines 2348--2349 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::read[]EMBL[]GenomicRegion[]file (file name) [53] Overfull \hbox (7.08008pt too wide) in paragraph at lines 2401--2402 []\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 2426--2427 []\OT1/cmtt/m/n/10 Wise2[]show[]pretty[]GenomicRegion (gr,show[]supporting,ofp) Overfull \hbox (59.57962pt too wide) in paragraph at lines 2427--2428 []\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::show[]pretty[]GenomicRegion (gr,show[ ]supporting,ofp) [54] [55] [56] Overfull \hbox (32.9967pt too wide) in paragraph at lines 2592--2592 [] \OT1/cmtt/m/n/10 b) cooperation with future versions of histogram.c would be possible.[] [57] [58] [59] Overfull \hbox (123.4428pt too wide) in paragraph at lines 2794--2795 []\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 2795--2796 []\OT1/cmtt/m/n/10 &Wise2::Histogram::set[]EVD (h,mu,lambda,lowbound,highbound, wonka,ndegrees) Overfull \hbox (33.66461pt too wide) in paragraph at lines 2797--2798 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->set[]EVD(mu,lambda,lowbound,highbound ,wonka,ndegrees) [60] [61] [62] Overfull \hbox (30.97293pt too wide) in paragraph at lines 2971--2972 []\OT1/cmr/m/n/10 should[]store Type [boolean (*should[]store)(int given[]score ,double in-ter-nal[]score[]level) [63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76] Overfull \hbox (16.34366pt too wide) in paragraph at lines 3839--3840 []\OT1/cmtt/m/n/10 Wise2[]force[]to[]dna[]Sequence (seq,fraction,number[]of[]co nver) [77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87] Overfull \hbox (24.01358pt too wide) in paragraph at lines 4508--4515 \OT1/cmr/m/n/10 have any se-quence in it. When se-quence is asked for by get[]P rotein[]from[]Translation() [88] [89] Overfull \hbox (62.7533pt too wide) in paragraph at lines 4609--4610 []\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 4610--4611 []\OT1/cmtt/m/n/10 &Wise2::make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap ,text,dpri) [90] Overfull \hbox (335.96082pt too wide) in paragraph at lines 4671--4672 []\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 4672--4673 []\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) [91] Overfull \hbox (329.87091pt too wide) in paragraph at lines 4698--4699 []\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 4699--4700 []\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) [92] Overfull \hbox (265.40146pt too wide) in paragraph at lines 4732--4733 []\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 4733--4734 []\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) [93] Overfull \hbox (47.00343pt too wide) in paragraph at lines 4780--4781 []\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 4781--4782 []\OT1/cmtt/m/n/10 &Wise2::protein2genomic[]ascii[]display (alb,p,gen,ct,name,m ain,ofp) [94] Overfull \hbox (188.7522pt too wide) in paragraph at lines 4801--4802 []\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 4802--4803 []\OT1/cmtt/m/n/10 &Wise2::protcdna[]ascii[]display (alb,protsequence,protname, protoff,cdna,ct,name,main,mult,ofp) [95] Overfull \hbox (1.40793pt too wide) in paragraph at lines 4893--4894 []\OT1/cmr/m/n/10 transition[GENEFREQUENCY21[]TRANSITION[]LEN] Type [dou-ble : Scalar] [96] [97] Overfull \hbox (71.7832pt too wide) in paragraph at lines 5014--5015 []\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 5015--5016 []\OT1/cmtt/m/n/10 &Wise2::MatchSummarySet::MatchSummarySet[]from[]AlnBlock[]es twise Overfull \hbox (62.22433pt too wide) in paragraph at lines 5017--5018 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->MatchSummarySet[]from[]AlnBlock[]estw ise(qname,offset,target) [98] Overfull \hbox (82.28311pt too wide) in paragraph at lines 5040--5041 []\OT1/cmtt/m/n/10 Wise2[]MatchSummarySet[]from[]AlnBlock[]genewise (alb,qname, protoff,target) Overfull \hbox (7.08008pt too wide) in paragraph at lines 5041--5042 []\OT1/cmtt/m/n/10 &Wise2::MatchSummarySet::MatchSummarySet[]from[]AlnBlock[]ge newise Overfull \hbox (72.72424pt too wide) in paragraph at lines 5043--5044 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->MatchSummarySet[]from[]AlnBlock[]gene wise(qname,protoff,target) [99] [100] Overfull \hbox (92.78302pt too wide) in paragraph at lines 5174--5175 []\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 5175--5176 []\OT1/cmtt/m/n/10 &Wise2::write[]pretty[]str[]align (alb,qname,query,tname,tar get,name,main,ofp) [101] Overfull \hbox (3.5338pt too wide) in paragraph at lines 5217--5218 []\OT1/cmtt/m/n/10 Wise2[]write[]pretty[]Protein[]align (alb,q,t,name,main,ofp) [102] Overfull \hbox (29.5499pt too wide) in paragraph at lines 5290--5291 []\OT1/cmtt/m/n/10 &Wise2::DnaSequenceHitList::read[]MSPcrunch[]DnaSequenceHitL ist (ifp) [103] Overfull \hbox (99.50298pt too wide) in paragraph at lines 5348--5349 []\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 5349--5350 []\OT1/cmtt/m/n/10 &Wise2::Align[]strings[]ProteinSmithWaterman (one,two,comp,g ap,ext,dpenv,dpri) [104] Overfull \hbox (110.00288pt too wide) in paragraph at lines 5373--5374 []\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 5374--5375 []\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 5386--5387 []\OT1/cmr/m/n/10 [OWNER] new AlnBlock struc-ture rep-re-sent-ing the align-men t [AlnBlock [105] Overfull \hbox (68.00325pt too wide) in paragraph at lines 5407--5408 []\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 5408--5409 []\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 5434--5435 []\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]ABC (one,two,comp,a,b,c,dpenv,dpri) [106] Overfull \hbox (47.00343pt too wide) in paragraph at lines 5455--5456 []\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 5456--5457 []\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 5471--5474 \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 5478--5479 []\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 5479--5480 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinSW (querydb,targetdb,comp,gap,e xt,bits[]cutoff,report[]level,die[]on[]error,dbsi) [107] Overfull \hbox (235.37173pt too wide) in paragraph at lines 5500--5501 []\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 5501--5502 []\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b, c,bits[]cutoff,report[]level,die[]on[]error,dbsi) [108] Overfull \hbox (359.90063pt too wide) in paragraph at lines 5523--5524 []\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 5524--5525 []\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) [109] Overfull \hbox (15.42177pt too wide) in paragraph at lines 5587--5588 []\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 5594--5595 []\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 5598--5599 []\OT1/cmr/m/n/10 index[]generic Type [Three-State-Model * (*in-dex[]generic)(T hreeStateDB *tdb,DataEntry [110] Overfull \hbox (29.5499pt too wide) in paragraph at lines 5669--5670 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateDB::new[]proteindb[]ThreeStateDB (sdb,comp ,gap,ext) [111] [112] [113] Overfull \hbox (16.10999pt too wide) in paragraph at lines 5802--5803 []\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 5822--5823 []\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 5823--5824 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::force[]weighted[]local[]model (tsm, prob[]into[]model,ratio[]start,ratio[]end) Overfull \hbox (93.09401pt too wide) in paragraph at lines 5825--5826 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->force[]weighted[]local[]model(prob[]i nto[]model,ratio[]start,ratio[]end) Overfull \hbox (49.31339pt too wide) in paragraph at lines 5845--5846 []\OT1/cmtt/m/n/10 Wise2[]ThreeStateModel[]from[]half[]bit[]Sequence (pro,mat,r m,gap,ext) [114] Overfull \hbox (5.61008pt too wide) in paragraph at lines 5846--5847 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::ThreeStateModel[]from[]half[]bit[]S equence Overfull \hbox (39.75452pt too wide) in paragraph at lines 5848--5849 []\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->ThreeStateModel[]from[]half[]bit[]Seq uence(mat,rm,gap,ext) Overfull \hbox (51.38966pt too wide) in paragraph at lines 5872--5873 []\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::write[]HMMer[]1[]7[]ascii[]ThreeSta teModel (tsm,ofp) [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, 318781 bytes). Transcript written on api.log. cd docs && pdflatex dynamite.tex This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./dynamite.tex LaTeX2e <2023-11-01> L3 programming layer <2023-11-09> (/usr/share/texlive/texmf-dist/tex/latex/base/latex209.def Entering LaTeX 2.09 COMPATIBILITY MODE ************************************************************* !!WARNING!! !!WARNING!! !!WARNING!! !!WARNING!! This mode attempts to provide an emulation of the LaTeX 2.09 author environment so that OLD documents can be successfully processed. It should NOT be used for NEW documents! New documents should use Standard LaTeX conventions and start with the \documentclass command. Compatibility mode is UNLIKELY TO WORK with LaTeX 2.09 style files that change any internal macros, especially not with those that change the FONT SELECTION or OUTPUT ROUTINES. Therefore such style files MUST BE UPDATED to use Current Standard LaTeX: LaTeX2e. If you suspect that you may be using such a style file, which is probably very, very old by now, then you should attempt to get it updated by sending a copy of this error message to the author of that file. ************************************************************* (/usr/share/texlive/texmf-dist/tex/latex/base/tracefnt.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/latexsym.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2023/05/17 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) No file dynamite.aux. (/usr/share/texlive/texmf-dist/tex/latex/base/ulasy.fd) [1{/var/lib/texmf/fonts /map/pdftex/updmap/pdftex.map}] No file dynamite.toc. [2] [3] LaTeX Warning: Reference `own_objects' on page 4 undefined on input line 77. [4] [5] [6] Overfull \hbox (4.11092pt too wide) in paragraph at lines 253--257 \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 588--588 [] \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 588--588 [] \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 588--588 [] \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 588--588 [] \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 588--588 [] \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 588--588 [] \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 588--588 [] \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 588--588 [] \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 588--588 [] \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 588--588 [] \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 588--588 [] \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 632--632 [] \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 632--632 [] \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 632--632 [] \OT1/cmtt/m/n/10 * If the sequences are small enough then it should use ex plicit memory.[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 632--632 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp ,-gap,-ext,NULL);[] [15] Overfull \hbox (80.24629pt too wide) in paragraph at lines 632--632 [] \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 639--639 [] \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 654--654 [] \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 738--738 []\OT1/cmtt/m/n/10 Q22037 EPENLRKIFVGGLTSNTTDDLMREFYSQFGEITDIIVMR DPTTKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 [] \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 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMR DPNTKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 GFVTFSGKTEVDAAMKQRPHIIDGKTVDPKRAVPRDDKN RSESNVSTKR[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 [] \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 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN GFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQ RPGAHLTVKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 LYVSGVREDHTEDMLTEYFTKYGTVTKSEIILDKATQKP RGFGFVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 [] \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 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKK RGFAFVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 HDSVDQCVLQKSHMVNGHRCDVRKGLSKDEMSKAQMNRD RETRGGRSRD[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 738--738 [] \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 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN HDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASAS---- -SSQRGRSGS[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 GQRGGYNGGG-GGGGGWGGPAQRGGPGAYGGP-GGGGQG GYGGDYGG--[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 738--738 [] \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 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN GNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSRGGGGYG GSGDGYNGFG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 GWGQQGGGGQGGWGGPQQQQGGG-GWGQQGGGGQGGWGG PQQQQQGGWG[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 738--738 [] \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 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN NDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSG-YGGSGS YDSYNNGGGR[] [17] [18] Overfull \hbox (48.88945pt too wide) in paragraph at lines 793--795 []\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] Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] [21] Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942 [] \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 942--942 [] \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 942--942 [] \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 1015--1019 \OT1/cmr/m/n/10 and GE-NOMIC[]INTRON. No-tice how the source lines to and from GE-NOMIC[]INSERT Overfull \hbox (38.24666pt too wide) in paragraph at lines 1116--1116 []\OT1/cmtt/m/n/10 #define DnaMatrix_Score(dnamat,base1,base2) (dnamat->score[b ase1][base2])[] [23] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1116--1116 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1342--1342 [] \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 1379--1379 [] \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 1379--1379 [] \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 1379--1379 [] \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 1379--1379 [] \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 1379--1379 [] \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 1379--1379 [] \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 1379--1379 [] \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 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 1 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GATGGT-TAT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GAT T T T[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2132 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GAT--TAT-T[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 49 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2178 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] [31] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 98 CAGTGGCAAGAAAAGGGGCTTTGCCT-TAGTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 CAGTGGCAAGAAAAGGGGCTTTGCCT T GTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2227 CAGTGGCAAGAAAAGGGGCTTTGCCTTT-GTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 146 CTCCGTGGATAAGATTGTCA TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 CTCCGTGGATAAGATTGTCA TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2275 CTCCGTGGATAAGATTGTCA<-2295:2387->TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 182 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2404 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 231 ATGGCTAGTGCTTCATCCAGCCAAAGAG GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 ATGGCTAGTGCTTCATCCAGCCAAAGAG GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2453 ATGGCTAGTGCTTCATCCAGCCAAAGAG<-2481:2566 ->GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 267 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2575 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2624 ACAACTTCGGTCGTGGAGGAAACTTCAGTGGTCGTG<-2 660:2793->[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 352 GTNG-CTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 GT G CTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2794 GT-GGCTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 400 ATGGCTATAATGGATTTGGCAATGATG GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 ATGGCTATAATGGATTTGGCAATGATG GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2842 ATGGCTATAATGGATTTGGCAATGATG<-2869:3805- >GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 436 TTGGAGGTGGTGGAAGCTACAATGATTTTGGG--tttat gcA-CAATCA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 TTGGAGGTGGTGGAAGCTACAATGATTTTGGG ++ + +A CAATCA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 3815 TTGGAGGTGGTGGAAGCTACAATGATTTTGGGAATT-A- -CAACAATCA[] [32] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 482 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 3861 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 531 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 3910 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 580 AAG GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 AAG GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 3959 AAG<-3962:4251->GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] [33] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1572--1572 []\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 1572--1572 []\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 1600--1600 []\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 1634--1634 [] \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 1634--1634 [] \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 1727--1727 []\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 1727--1727 []\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 1849--1849 []\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 1849--1849 []\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 1849--1849 [] \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 1911--1912 []\OT1/cmr/m/n/10 The macro Dna-Ma-trix[]Score which is de-fined at the top of the cdna2genomic.dy Overfull \hbox (17.24684pt too wide) in paragraph at lines 1928--1928 [] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,i),GENOMIC_CODON(ta rget,j))"[] [42] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1944--1944 [] \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 1955--1955 [] \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 1967--1967 [] \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 1967--1967 []\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 2014--2014 [] \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 2014--2014 [] \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 2255--2255 [] \OT1/cmtt/m/n/10 fprintf(stdout,"dbsearch [options] \n");[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 2255--2255 [] \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 2255--2255 [] \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 2255--2255 [] \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 2255--2255 [] \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 2255--2255 [] \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 2255--2255 [] \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 2255--2255 [] \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 2255--2255 [] \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 2255--2255 [] \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 2255--2255 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (174.74547pt too wide) in paragraph at lines 2255--2255 [] \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 2255--2255 [] \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta rget);[] [48] Overfull \hbox (74.99634pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s",t emp->baseseq->name);[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs, mat,-12,-2,NULL);[] Overfull \hbox (101.24611pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query->n ame,temp->baseseq->name);[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 2255--2255 [] \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 2263--2263 [] \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 2263--2263 [] \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 2292--2292 [] \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 2528--2534 \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 2772--2776 \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 2792--2792 [] \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 2792--2792 [] \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, 221219 bytes). Transcript written on dynamite.log. cd docs && pdflatex dynamite.tex This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./dynamite.tex LaTeX2e <2023-11-01> L3 programming layer <2023-11-09> (/usr/share/texlive/texmf-dist/tex/latex/base/latex209.def Entering LaTeX 2.09 COMPATIBILITY MODE ************************************************************* !!WARNING!! !!WARNING!! !!WARNING!! !!WARNING!! This mode attempts to provide an emulation of the LaTeX 2.09 author environment so that OLD documents can be successfully processed. It should NOT be used for NEW documents! New documents should use Standard LaTeX conventions and start with the \documentclass command. Compatibility mode is UNLIKELY TO WORK with LaTeX 2.09 style files that change any internal macros, especially not with those that change the FONT SELECTION or OUTPUT ROUTINES. Therefore such style files MUST BE UPDATED to use Current Standard LaTeX: LaTeX2e. If you suspect that you may be using such a style file, which is probably very, very old by now, then you should attempt to get it updated by sending a copy of this error message to the author of that file. ************************************************************* (/usr/share/texlive/texmf-dist/tex/latex/base/tracefnt.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/latexsym.sty)) (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2023/05/17 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./dynamite.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ulasy.fd) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./dynamite.toc [2] Overfull \hbox (8.02837pt too wide) in paragraph at lines 50--50 [][] []\OT1/cmr/m/n/10 [Dynamite Level] Did not un-der-stand line [ source MAT CH]. ) [3] [4] [5] [6] [7] [8] Overfull \hbox (4.11092pt too wide) in paragraph at lines 253--257 \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 588--588 [] \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 588--588 [] \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 588--588 [] \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 588--588 [] \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 588--588 [] \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 588--588 [] \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 588--588 [] \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 588--588 [] \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 588--588 [] \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 588--588 [] \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 588--588 [] \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 632--632 [] \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 632--632 [] \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 632--632 [] \OT1/cmtt/m/n/10 * If the sequences are small enough then it should use ex plicit memory.[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 632--632 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp ,-gap,-ext,NULL);[] [17] Overfull \hbox (80.24629pt too wide) in paragraph at lines 632--632 [] \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 639--639 [] \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 654--654 [] \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 738--738 []\OT1/cmtt/m/n/10 Q22037 EPENLRKIFVGGLTSNTTDDLMREFYSQFGEITDIIVMR DPTTKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 [] \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 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMR DPNTKRSRGF[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 GFVTFSGKTEVDAAMKQRPHIIDGKTVDPKRAVPRDDKN RSESNVSTKR[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 [] \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 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN GFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQ RPGAHLTVKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 LYVSGVREDHTEDMLTEYFTKYGTVTKSEIILDKATQKP RGFGFVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 [] \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 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKK RGFAFVTFDD[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 HDSVDQCVLQKSHMVNGHRCDVRKGLSKDEMSKAQMNRD RETRGGRSRD[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 738--738 [] \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 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN HDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASAS---- -SSQRGRSGS[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 GQRGGYNGGG-GGGGGWGGPAQRGGPGAYGGP-GGGGQG GYGGDYGG--[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 738--738 [] \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 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN GNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSRGGGGYG GSGDGYNGFG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738 []\OT1/cmtt/m/n/10 Q22037 GWGQQGGGGQGGWGGPQQQQGGG-GWGQQGGGGQGGWGG PQQQQQGGWG[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 738--738 [] \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 738--738 []\OT1/cmtt/m/n/10 ROA1_HUMAN NDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSG-YGGSGS YDSYNNGGGR[] [19] [20] Overfull \hbox (48.88945pt too wide) in paragraph at lines 793--795 []\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] Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942 [] \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta rget,j))"[] [23] Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942 [] \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 942--942 [] \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 942--942 [] \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 1015--1019 \OT1/cmr/m/n/10 and GE-NOMIC[]INTRON. No-tice how the source lines to and from GE-NOMIC[]INSERT Overfull \hbox (38.24666pt too wide) in paragraph at lines 1116--1116 []\OT1/cmtt/m/n/10 #define DnaMatrix_Score(dnamat,base1,base2) (dnamat->score[b ase1][base2])[] [25] Overfull \hbox (11.99689pt too wide) in paragraph at lines 1116--1116 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1335--1335 [] \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 1342--1342 [] \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 1379--1379 [] \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 1379--1379 [] \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 1379--1379 [] \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 1379--1379 [] \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 1379--1379 [] \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 1379--1379 [] \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 1379--1379 [] \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 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 1 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GATGGT-TAT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GAT T T T[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2132 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA GAT--TAT-T[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 49 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2178 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA CTGACCGAGG[] [33] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 98 CAGTGGCAAGAAAAGGGGCTTTGCCT-TAGTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 CAGTGGCAAGAAAAGGGGCTTTGCCT T GTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2227 CAGTGGCAAGAAAAGGGGCTTTGCCTTT-GTAACCTTTG ACGACCATGA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 146 CTCCGTGGATAAGATTGTCA TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 CTCCGTGGATAAGATTGTCA TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2275 CTCCGTGGATAAGATTGTCA<-2295:2387->TTCAGA AATACCATAC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 182 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2404 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC AAAGCAAGAG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 231 ATGGCTAGTGCTTCATCCAGCCAAAGAG GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 ATGGCTAGTGCTTCATCCAGCCAAAGAG GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2453 ATGGCTAGTGCTTCATCCAGCCAAAGAG<-2481:2566 ->GTCGAAGT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 267 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2575 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC GGTGGGAATG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2624 ACAACTTCGGTCGTGGAGGAAACTTCAGTGGTCGTG<-2 660:2793->[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 352 GTNG-CTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 GT G CTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2794 GT-GGCTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT GGCAGTGGGG[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 400 ATGGCTATAATGGATTTGGCAATGATG GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 ATGGCTATAATGGATTTGGCAATGATG GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 2842 ATGGCTATAATGGATTTGGCAATGATG<-2869:3805- >GAAGCAATT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 436 TTGGAGGTGGTGGAAGCTACAATGATTTTGGG--tttat gcA-CAATCA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 TTGGAGGTGGTGGAAGCTACAATGATTTTGGG ++ + +A CAATCA[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 3815 TTGGAGGTGGTGGAAGCTACAATGATTTTGGGAATT-A- -CAACAATCA[] [34] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 482 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 3861 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG AGGCAGAAGC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 531 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 3910 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA CCACGAAACC[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNCPA1 580 AAG GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 [] \OT1/cmtt/m/n/10 AAG GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465 []\OT1/cmtt/m/n/10 HSHNRNPA 3959 AAG<-3962:4251->GTGGCTATGGCGGTTCCAGCAGC AGCAGTAGCT[] [35] Overfull \hbox (22.4968pt too wide) in paragraph at lines 1572--1572 []\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 1572--1572 []\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 1600--1600 []\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 1634--1634 [] \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 1634--1634 [] \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 1727--1727 []\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 1727--1727 []\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 1849--1849 []\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 1849--1849 []\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 1849--1849 [] \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 1911--1912 []\OT1/cmr/m/n/10 The macro Dna-Ma-trix[]Score which is de-fined at the top of the cdna2genomic.dy Overfull \hbox (17.24684pt too wide) in paragraph at lines 1928--1928 [] \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,i),GENOMIC_CODON(ta rget,j))"[] [44] Overfull \hbox (53.99652pt too wide) in paragraph at lines 1944--1944 [] \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 1955--1955 [] \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 1967--1967 [] \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 1967--1967 []\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 2014--2014 [] \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 2014--2014 [] \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 2255--2255 [] \OT1/cmtt/m/n/10 fprintf(stdout,"dbsearch [options] \n");[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 2255--2255 [] \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 2255--2255 [] \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 2255--2255 [] \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 2255--2255 [] \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 2255--2255 [] \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 2255--2255 [] \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 2255--2255 [] \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 2255--2255 [] \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 2255--2255 [] \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 2255--2255 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s ",query->name);[] Overfull \hbox (174.74547pt too wide) in paragraph at lines 2255--2255 [] \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 2255--2255 [] \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta rget);[] [50] Overfull \hbox (74.99634pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s",t emp->baseseq->name);[] Overfull \hbox (59.24648pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs, mat,-12,-2,NULL);[] Overfull \hbox (101.24611pt too wide) in paragraph at lines 2255--2255 [] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query->n ame,temp->baseseq->name);[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 2255--2255 [] \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 2263--2263 [] \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 2263--2263 [] \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 2292--2292 [] \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 2528--2534 \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 2772--2776 \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 2792--2792 [] \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 2792--2792 [] \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, 224783 bytes). Transcript written on dynamite.log. cd docs && pdflatex wise2.tex This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./wise2.tex LaTeX2e <2023-11-01> L3 programming layer <2023-11-09> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2023/05/17 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) No file wise2.aux. (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] No file wise2.toc. [2] [3] [4] LaTeX Warning: Reference `genewise_large' on page 5 undefined on input line 110 . LaTeX Warning: Reference `estwise_large' on page 5 undefined on input line 113. Overfull \hbox (11.99689pt too wide) in paragraph at lines 206--206 []\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 206--206 []\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 206--206 []\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 206--206 []\OT1/cmtt/m/n/10 roa1_drome 88 AQKSRPHKIDGRVVEPKRAVPRQ DID[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 A +RPHK+DGRVVEPKRAV R+ D[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 AMNARPHKVDGRVVEPKRAVSRE DSQ[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 HSHNRNPA 1867 gaagaccagggagggcaaggtagGTGAGTG Intron 2 TAGgtc[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 ctacgcaataggttacagctcga<0-----[1936 : 2 083]-0>aca[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 tgtagacggtaatgaagatccaa tta[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 roa1_drome 114 SPNAGATVKKLFVGALKDDHDEQSIRDYFQHFGNIVDIN IVIDKETGKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \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 206--206 [] \OT1/cmtt/m/n/10 RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIE IMTDRGSGKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 HSHNRNPA 2093 acggctagaaatgggaaggaggcccagttgctgaaggag aaagcgagaa[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 gcgcatctaatttggtaaacaaaatgaataaagatatta ttcaggggaa[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 aatccatgagatttctaactaatcaatttagtaatagta cgtcactcga[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 roa1_drome 163 RGFAFVEFDDYDPVDKVV QKQHQ[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 RGFAFV FDD+D VDK+V QK H[] [6] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 RGFAFVTFDDHDSVDKIV L:I[att] QKYHT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 HSHNRNPA 2240 agtgtgatggcgtggaagAGTAAGTA Intron 3 TAGTTcatca[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 ggtcttctaaaactaatt <1-----[2295 : 2387] -1> aaaac[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 gctctactcctccgtgtc gactt[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 tagaagatgactcaaatcgcccgag <1-----[2481 : 2793][] [7] [8] LaTeX Warning: Reference `sec:start_end' on page 9 undefined on input line 297. [9] LaTeX Warning: Reference `half_and_blast' on page 10 undefined on input line 34 6. [10] [11] LaTeX Warning: Reference `genewise_large' on page 12 undefined on input line 45 5. LaTeX Warning: Reference `estwise_large' on page 12 undefined on input line 455 . LaTeX Warning: Reference `compile_pthread' on page 12 undefined on input line 4 66. LaTeX Warning: Reference `half_and_blast' on page 12 undefined on input line 47 3. [12] LaTeX Warning: Reference `half_and_blast' on page 13 undefined on input line 51 3. [13] [14] LaTeX Warning: Reference `running_pthread' on page 15 undefined on input line 6 13. [15] [16] [17] LaTeX Warning: Reference `Figure:genewise21' on page 18 undefined on input line 708. [18] [19] [20] LaTeX Warning: Reference `Figure:genewise623' on page 21 undefined on input lin e 900. [21] Overfull \hbox (2.03789pt too wide) in paragraph at lines 965--968 []\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 1108--1109 []\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 81. [27] LaTeX Warning: Reference `sec:start_end' on page 28 undefined on input line 121 0. [28] Overfull \hbox (42.24687pt too wide) in paragraph at lines 1268--1268 []\OT1/cmtt/m/n/10 pexon [] Overfull \hbox (42.24687pt too wide) in paragraph at lines 1268--1268 []\OT1/cmtt/m/n/10 pexon [] [29] LaTeX Warning: Reference `sec:alg' on page 30 undefined on input line 1276. Overfull \hbox (36.99692pt too wide) in paragraph at lines 1312--1312 []\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 1312--1312 []\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 7. [32] [33] [34] LaTeX Warning: Reference `sec:start_end' on page 35 undefined on input line 146 9. [35] [36] LaTeX Warning: Reference `compile_pthread' on page 37 undefined on input line 1 561. [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, 213078 bytes). Transcript written on wise2.log. cd docs && pdflatex wise2.tex This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./wise2.tex LaTeX2e <2023-11-01> L3 programming layer <2023-11-09> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2023/05/17 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty) (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg) (/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def))) (/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def) (./wise2.aux) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./wise2.toc [2]) [3] [4] [5] Overfull \hbox (11.99689pt too wide) in paragraph at lines 206--206 []\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 206--206 []\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 206--206 []\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 206--206 []\OT1/cmtt/m/n/10 roa1_drome 88 AQKSRPHKIDGRVVEPKRAVPRQ DID[] Overfull \hbox (11.99689pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 A +RPHK+DGRVVEPKRAV R+ D[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 AMNARPHKVDGRVVEPKRAVSRE DSQ[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 HSHNRNPA 1867 gaagaccagggagggcaaggtagGTGAGTG Intron 2 TAGgtc[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 ctacgcaataggttacagctcga<0-----[1936 : 2 083]-0>aca[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 tgtagacggtaatgaagatccaa tta[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 roa1_drome 114 SPNAGATVKKLFVGALKDDHDEQSIRDYFQHFGNIVDIN IVIDKETGKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \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 206--206 [] \OT1/cmtt/m/n/10 RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIE IMTDRGSGKK[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 HSHNRNPA 2093 acggctagaaatgggaaggaggcccagttgctgaaggag aaagcgagaa[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 gcgcatctaatttggtaaacaaaatgaataaagatatta ttcaggggaa[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 aatccatgagatttctaactaatcaatttagtaatagta cgtcactcga[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 roa1_drome 163 RGFAFVEFDDYDPVDKVV QKQHQ[] Overfull \hbox (17.24684pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 RGFAFV FDD+D VDK+V QK H[] [7] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 RGFAFVTFDDHDSVDKIV L:I[att] QKYHT[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 []\OT1/cmtt/m/n/10 HSHNRNPA 2240 agtgtgatggcgtggaagAGTAAGTA Intron 3 TAGTTcatca[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 ggtcttctaaaactaatt <1-----[2295 : 2387] -1> aaaac[] Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 gctctactcctccgtgtc gactt[] Overfull \hbox (6.74693pt too wide) in paragraph at lines 206--206 [] \OT1/cmtt/m/n/10 tagaagatgactcaaatcgcccgag <1-----[2481 : 2793][] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] LaTeX Warning: Reference `Figure:genewise21' on page 19 undefined on input line 708. [19] [20] [21] [22] Overfull \hbox (2.03789pt too wide) in paragraph at lines 965--968 []\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 1108--1109 []\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 1268--1268 []\OT1/cmtt/m/n/10 pexon [] Overfull \hbox (42.24687pt too wide) in paragraph at lines 1268--1268 []\OT1/cmtt/m/n/10 pexon [] [30] Overfull \hbox (36.99692pt too wide) in paragraph at lines 1312--1312 []\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 1312--1312 []\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, 215377 bytes). Transcript written on wise2.log. cd docs && hevea api.tex ./api.tex:2: Warning: Command not found: \pdftrailerid ./api.tex:233: Warning: Undefined label: 'object_GeneFrequency' ./api.tex:236: Warning: Undefined label: 'module_gwrap' ./api.tex:237: Warning: Undefined label: 'module_gwrap' ./api.tex:238: Warning: Undefined label: 'module_gwrap' ./api.tex:239: Warning: Undefined label: 'module_gwrap' ./api.tex:389: Warning: Undefined label: 'module_gwrap' ./api.tex:426: Warning: Undefined label: 'module_codonmat' ./api.tex:435: Warning: Undefined label: 'module_dbimpl' ./api.tex:476: Warning: Application of '\'' on ',' failed ./api.tex:629: Warning: Application of '\'' on 't' failed ./api.tex:631: Warning: Application of '\'' on 'b' failed ./api.tex:633: Warning: Application of '\'' on 'b' failed ./api.tex:1642: Warning: Application of '\'' on 't' failed ./api.tex:1660: Warning: Application of '\'' on 't' failed ./api.tex:1882: Warning: Application of '\'' on '.' failed ./api.tex:2441: Warning: Application of '\'' on 'b' failed ./api.tex:2847: Warning: Application of '\'' on 'h' failed ./api.tex:2847: Warning: Application of '\'' on 't' failed ./api.tex:4435: Warning: Application of '\'' on '.' failed ./api.tex:4952: Warning: Application of '\'' on 'd' failed ./api.tex:4952: Warning: Application of '\'' on 'd' failed ./api.tex:5809: Warning: Application of '\'' on 'f' failed ./api.tex:5809: Warning: Application of '\'' on '[' failed ./api.tex:5830: Warning: Application of '\'' on 'f' failed ./api.tex:5830: Warning: Application of '\'' on '[' failed cd docs && hevea api.tex ./api.tex:2: Warning: Command not found: \pdftrailerid ./api.tex:233: Warning: Undefined label: 'object_GeneFrequency' ./api.tex:236: Warning: Undefined label: 'module_gwrap' ./api.tex:237: Warning: Undefined label: 'module_gwrap' ./api.tex:238: Warning: Undefined label: 'module_gwrap' ./api.tex:239: Warning: Undefined label: 'module_gwrap' ./api.tex:389: Warning: Undefined label: 'module_gwrap' ./api.tex:426: Warning: Undefined label: 'module_codonmat' ./api.tex:435: Warning: Undefined label: 'module_dbimpl' ./api.tex:476: Warning: Application of '\'' on ',' failed ./api.tex:629: Warning: Application of '\'' on 't' failed ./api.tex:631: Warning: Application of '\'' on 'b' failed ./api.tex:633: Warning: Application of '\'' on 'b' failed ./api.tex:1642: Warning: Application of '\'' on 't' failed ./api.tex:1660: Warning: Application of '\'' on 't' failed ./api.tex:1882: Warning: Application of '\'' on '.' failed ./api.tex:2441: Warning: Application of '\'' on 'b' failed ./api.tex:2847: Warning: Application of '\'' on 'h' failed ./api.tex:2847: Warning: Application of '\'' on 't' failed ./api.tex:4435: Warning: Application of '\'' on '.' failed ./api.tex:4952: Warning: Application of '\'' on 'd' failed ./api.tex:4952: Warning: Application of '\'' on 'd' failed ./api.tex:5809: Warning: Application of '\'' on 'f' failed ./api.tex:5809: Warning: Application of '\'' on '[' failed ./api.tex:5830: Warning: Application of '\'' on 'f' failed ./api.tex:5830: Warning: Application of '\'' on '[' failed cd docs && hevea dynamite.tex ./dynamite.tex:2: Warning: Command not found: \pdftrailerid ./dynamite.tex:2618: Warning: Command not found: \+ ./dynamite.tex:2618: Warning: Command not found: \* ./dynamite.tex:2619: Warning: Command not found: \* ./dynamite.tex:2756: Warning: Application of '\"' on ')' failed ./dynamite.tex:2756: Warning: Application of '\"' on ')' failed cd docs && hevea dynamite.tex ./dynamite.tex:2: Warning: Command not found: \pdftrailerid ./dynamite.tex:2618: Warning: Command not found: \+ ./dynamite.tex:2618: Warning: Command not found: \* ./dynamite.tex:2619: Warning: Command not found: \* ./dynamite.tex:2756: Warning: Application of '\"' on ')' failed ./dynamite.tex:2756: Warning: Application of '\"' on ')' failed cd docs && hevea wise2.tex ./wise2.tex:3: Warning: Command not found: \pdftrailerid ./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:255: 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:277: Warning: \hbox ./wise2.tex:708: Warning: Undefined label: 'Figure:genewise21' ./wise2.tex:712: Warning: Command not found: \leavevmode ./wise2.tex:904: Warning: Command not found: \leavevmode cd docs && hevea wise2.tex ./wise2.tex:3: Warning: Command not found: \pdftrailerid ./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:255: 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:277: Warning: \hbox ./wise2.tex:708: Warning: Undefined label: 'Figure:genewise21' ./wise2.tex:712: Warning: Command not found: \leavevmode ./wise2.tex:904: Warning: Command not found: \leavevmode mkdir -p docs/api mkdir -p docs/dynamite mkdir -p docs/wise2 mv docs/api.html docs/api mv docs/dynamite.html docs/dynamite mv docs/wise2.html docs/wise2 dh_auto_build make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep -a rm -f -- debian/wise.substvars rm -fr -- debian/.debhelper/generated/wise/ debian/wise/ debian/tmp/ dh_installdirs -a install -m0755 -d debian/wise/usr/bin dh_install -a install -m0755 -d debian/wise/usr/bin cp --reflink=auto -a ./src/bin/dba ./src/bin/dnal ./src/bin/estwise ./src/bin/estwisedb ./src/bin/genewise ./src/bin/genewisedb ./src/bin/promoterwise ./src/bin/psw ./src/bin/pswdb ./src/bin/scanwise ./src/bin/scanwise_server ./src/models/genomewise debian/wise/usr/bin/ dh_installdocs -a install -m0755 -d debian/wise/usr/share/doc/wise install -m0755 -d debian/wise/usr/share/doc/wise cp --reflink=auto -a ./README debian/wise/usr/share/doc/wise cp --reflink=auto -a ./debian/tests/run-unit-test debian/wise/usr/share/doc/wise chmod -R u\+rw,go=rX debian/wise/usr/share/doc install -p -m0644 debian/README.Debian debian/wise/usr/share/doc/wise/README.Debian install -p -m0644 debian/copyright debian/wise/usr/share/doc/wise/copyright dh_installchangelogs -a install -m0755 -d debian/wise/usr/share/doc/wise install -p -m0644 debian/.debhelper/generated/wise/dh_installchangelogs.dch.trimmed debian/wise/usr/share/doc/wise/changelog.Debian dh_installexamples -a dh_installman -a install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/dba.1 debian/wise/usr/share/man/man1/dba.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/dnal.1 debian/wise/usr/share/man/man1/dnal.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/estwise.1 debian/wise/usr/share/man/man1/estwise.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/estwisedb.1 debian/wise/usr/share/man/man1/estwisedb.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/genewise.1 debian/wise/usr/share/man/man1/genewise.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/genewisedb.1 debian/wise/usr/share/man/man1/genewisedb.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/genomewise.1 debian/wise/usr/share/man/man1/genomewise.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/promoterwise.1 debian/wise/usr/share/man/man1/promoterwise.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/psw.1 debian/wise/usr/share/man/man1/psw.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/pswdb.1 debian/wise/usr/share/man/man1/pswdb.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/scanwise.1 debian/wise/usr/share/man/man1/scanwise.1 install -m0755 -d debian/wise/usr/share/man/man1/ install -p -m0644 ./debian/manpages.d/scanwise_server.1 debian/wise/usr/share/man/man1/scanwise_server.1 man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/dba.1 debian/wise/usr/share/man/man1/dnal.1 debian/wise/usr/share/man/man1/estwise.1 debian/wise/usr/share/man/man1/estwisedb.1 debian/wise/usr/share/man/man1/genewise.1 debian/wise/usr/share/man/man1/genewisedb.1 debian/wise/usr/share/man/man1/genomewise.1 debian/wise/usr/share/man/man1/promoterwise.1 debian/wise/usr/share/man/man1/psw.1 debian/wise/usr/share/man/man1/pswdb.1 debian/wise/usr/share/man/man1/scanwise.1 debian/wise/usr/share/man/man1/scanwise_server.1 mv debian/wise/usr/share/man/man1/dba.1.dh-new debian/wise/usr/share/man/man1/dba.1 mv debian/wise/usr/share/man/man1/dnal.1.dh-new debian/wise/usr/share/man/man1/dnal.1 mv debian/wise/usr/share/man/man1/estwise.1.dh-new debian/wise/usr/share/man/man1/estwise.1 mv debian/wise/usr/share/man/man1/estwisedb.1.dh-new debian/wise/usr/share/man/man1/estwisedb.1 mv debian/wise/usr/share/man/man1/genewise.1.dh-new debian/wise/usr/share/man/man1/genewise.1 mv debian/wise/usr/share/man/man1/genewisedb.1.dh-new debian/wise/usr/share/man/man1/genewisedb.1 mv debian/wise/usr/share/man/man1/genomewise.1.dh-new debian/wise/usr/share/man/man1/genomewise.1 mv debian/wise/usr/share/man/man1/promoterwise.1.dh-new debian/wise/usr/share/man/man1/promoterwise.1 mv debian/wise/usr/share/man/man1/psw.1.dh-new debian/wise/usr/share/man/man1/psw.1 mv debian/wise/usr/share/man/man1/pswdb.1.dh-new debian/wise/usr/share/man/man1/pswdb.1 mv debian/wise/usr/share/man/man1/scanwise.1.dh-new debian/wise/usr/share/man/man1/scanwise.1 mv debian/wise/usr/share/man/man1/scanwise_server.1.dh-new debian/wise/usr/share/man/man1/scanwise_server.1 chmod 0644 -- debian/wise/usr/share/man/man1/dba.1 debian/wise/usr/share/man/man1/dnal.1 debian/wise/usr/share/man/man1/estwise.1 debian/wise/usr/share/man/man1/estwisedb.1 debian/wise/usr/share/man/man1/genewise.1 debian/wise/usr/share/man/man1/genewisedb.1 debian/wise/usr/share/man/man1/genomewise.1 debian/wise/usr/share/man/man1/promoterwise.1 debian/wise/usr/share/man/man1/psw.1 debian/wise/usr/share/man/man1/pswdb.1 debian/wise/usr/share/man/man1/scanwise.1 debian/wise/usr/share/man/man1/scanwise_server.1 dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a cd debian/wise chmod a-x usr/share/doc/wise/changelog.Debian usr/share/man/man1/dba.1 usr/share/man/man1/dnal.1 usr/share/man/man1/estwise.1 usr/share/man/man1/estwisedb.1 usr/share/man/man1/genewise.1 usr/share/man/man1/genewisedb.1 usr/share/man/man1/genomewise.1 usr/share/man/man1/promoterwise.1 usr/share/man/man1/psw.1 usr/share/man/man1/pswdb.1 usr/share/man/man1/scanwise.1 usr/share/man/man1/scanwise_server.1 gzip -9nf usr/share/doc/wise/changelog.Debian usr/share/man/man1/dba.1 usr/share/man/man1/dnal.1 usr/share/man/man1/estwise.1 usr/share/man/man1/estwisedb.1 usr/share/man/man1/genewise.1 usr/share/man/man1/genewisedb.1 usr/share/man/man1/genomewise.1 usr/share/man/man1/promoterwise.1 usr/share/man/man1/psw.1 usr/share/man/man1/pswdb.1 usr/share/man/man1/scanwise.1 usr/share/man/man1/scanwise_server.1 cd '/<>' rm -f debian/wise.debhelper.log debian/rules override_dh_fixperms make[1]: Entering directory '/<>' dh_fixperms find debian/wise ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/wise/usr/share/doc -type f -a -true -a ! -regex 'debian/wise/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/wise/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/wise/usr/share/man -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/wise -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/wise/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x find debian -iname "*.hmm" -exec chmod -x \{\} \; make[1]: Leaving directory '/<>' dh_missing -a dh_dwz -a install -m0755 -d debian/wise/usr/lib/debug/.dwz/aarch64-linux-gnu dwz -mdebian/wise/usr/lib/debug/.dwz/aarch64-linux-gnu/wise.debug -M/usr/lib/debug/.dwz/aarch64-linux-gnu/wise.debug -- debian/wise/usr/bin/dba debian/wise/usr/bin/dnal debian/wise/usr/bin/estwise debian/wise/usr/bin/estwisedb debian/wise/usr/bin/genewise debian/wise/usr/bin/genewisedb debian/wise/usr/bin/genomewise debian/wise/usr/bin/promoterwise debian/wise/usr/bin/psw debian/wise/usr/bin/pswdb debian/wise/usr/bin/scanwise debian/wise/usr/bin/scanwise_server aarch64-linux-gnu-objcopy --compress-debug-sections debian/wise/usr/lib/debug/.dwz/aarch64-linux-gnu/wise.debug chmod 0644 -- debian/wise/usr/lib/debug/.dwz/aarch64-linux-gnu/wise.debug dh_strip -a install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/8a aarch64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genewisedb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/8a/ac7b73619c730de2169bfccb13008ed2f8afe9.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/8a/ac7b73619c730de2169bfccb13008ed2f8afe9.debug aarch64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genewisedb aarch64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/8a/ac7b73619c730de2169bfccb13008ed2f8afe9.debug debian/wise/usr/bin/genewisedb install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/15 aarch64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genewise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/15/b1e39bfe0c57dc068f60bd18f0f10b411b4033.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/15/b1e39bfe0c57dc068f60bd18f0f10b411b4033.debug aarch64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genewise aarch64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/15/b1e39bfe0c57dc068f60bd18f0f10b411b4033.debug debian/wise/usr/bin/genewise install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fe aarch64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/estwisedb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fe/9d6c8e46fcde5a67847fe1d1e48dbb4791f001.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fe/9d6c8e46fcde5a67847fe1d1e48dbb4791f001.debug aarch64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/estwisedb aarch64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fe/9d6c8e46fcde5a67847fe1d1e48dbb4791f001.debug debian/wise/usr/bin/estwisedb install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/29 aarch64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/estwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/29/cff3c402d3391f7ba45081fa4ae7f8c97bdcdd.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/29/cff3c402d3391f7ba45081fa4ae7f8c97bdcdd.debug aarch64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/estwise aarch64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/29/cff3c402d3391f7ba45081fa4ae7f8c97bdcdd.debug debian/wise/usr/bin/estwise install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/80 aarch64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/scanwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/80/ef38b40ad409f83410a468630df328bd41c3fd.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/80/ef38b40ad409f83410a468630df328bd41c3fd.debug aarch64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/scanwise aarch64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/80/ef38b40ad409f83410a468630df328bd41c3fd.debug debian/wise/usr/bin/scanwise install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/14 aarch64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/scanwise_server debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/14/410329288faccb18fe258e9d1249dc468e120e.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/14/410329288faccb18fe258e9d1249dc468e120e.debug aarch64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/scanwise_server aarch64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/14/410329288faccb18fe258e9d1249dc468e120e.debug debian/wise/usr/bin/scanwise_server install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/74 aarch64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/pswdb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/74/69eedc1e1e9bdc30266552ad7494daf21fe612.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/74/69eedc1e1e9bdc30266552ad7494daf21fe612.debug aarch64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/pswdb aarch64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/74/69eedc1e1e9bdc30266552ad7494daf21fe612.debug debian/wise/usr/bin/pswdb install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/bb aarch64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/psw debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/bb/f4620447bf052bd40435fd1f541030658fd129.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/bb/f4620447bf052bd40435fd1f541030658fd129.debug aarch64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/psw aarch64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/bb/f4620447bf052bd40435fd1f541030658fd129.debug debian/wise/usr/bin/psw install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/7c aarch64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/promoterwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/7c/ba31a03f4c94c0a7360127dd506126170a654b.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/7c/ba31a03f4c94c0a7360127dd506126170a654b.debug aarch64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/promoterwise aarch64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/7c/ba31a03f4c94c0a7360127dd506126170a654b.debug debian/wise/usr/bin/promoterwise install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/4b aarch64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genomewise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/4b/4bc36b0b0ea0723103707527196f9dd48d4dc7.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/4b/4bc36b0b0ea0723103707527196f9dd48d4dc7.debug aarch64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genomewise aarch64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/4b/4bc36b0b0ea0723103707527196f9dd48d4dc7.debug debian/wise/usr/bin/genomewise install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/c6 aarch64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/dba debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/c6/cf1fc45077ed479d854a80a0ede0eda457e18c.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/c6/cf1fc45077ed479d854a80a0ede0eda457e18c.debug aarch64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/dba aarch64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/c6/cf1fc45077ed479d854a80a0ede0eda457e18c.debug debian/wise/usr/bin/dba install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/17 aarch64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/dnal debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/17/a3e050be221b68cab21de6f8e5f9284cac0f35.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/17/a3e050be221b68cab21de6f8e5f9284cac0f35.debug aarch64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/dnal aarch64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/17/a3e050be221b68cab21de6f8e5f9284cac0f35.debug debian/wise/usr/bin/dnal install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/wise/usr/lib/debug/.dwz/aarch64-linux-gnu debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/wise/usr/lib/debug/.dwz rmdir -p --ignore-fail-on-non-empty debian/wise/usr/lib/debug install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/share/doc ln -s wise debian/.debhelper/wise/dbgsym-root/usr/share/doc/wise-dbgsym install -m0755 -d debian/.debhelper/wise dh_makeshlibs -a rm -f debian/wise/DEBIAN/shlibs dh_shlibdeps -a install -m0755 -d debian/wise/DEBIAN dpkg-shlibdeps -Tdebian/wise.substvars debian/wise/usr/bin/genewisedb debian/wise/usr/bin/genewise debian/wise/usr/bin/estwisedb debian/wise/usr/bin/estwise debian/wise/usr/bin/scanwise debian/wise/usr/bin/scanwise_server debian/wise/usr/bin/pswdb debian/wise/usr/bin/psw debian/wise/usr/bin/promoterwise debian/wise/usr/bin/genomewise debian/wise/usr/bin/dba debian/wise/usr/bin/dnal dh_installdeb -a install -m0755 -d debian/wise/DEBIAN dh_gencontrol -a install -m0755 -d debian/wise/DEBIAN echo misc:Depends= >> debian/wise.substvars echo misc:Pre-Depends= >> debian/wise.substvars install -m0755 -d debian/.debhelper/wise/dbgsym-root/DEBIAN dpkg-gencontrol -pwise -ldebian/changelog -Tdebian/wise.substvars -Pdebian/.debhelper/wise/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=wise-dbgsym "-DDepends=wise (= \${binary:Version})" "-DDescription=debug symbols for wise" "-DBuild-Ids=14410329288faccb18fe258e9d1249dc468e120e 15b1e39bfe0c57dc068f60bd18f0f10b411b4033 17a3e050be221b68cab21de6f8e5f9284cac0f35 29cff3c402d3391f7ba45081fa4ae7f8c97bdcdd 4b4bc36b0b0ea0723103707527196f9dd48d4dc7 7469eedc1e1e9bdc30266552ad7494daf21fe612 7cba31a03f4c94c0a7360127dd506126170a654b 80ef38b40ad409f83410a468630df328bd41c3fd 8aac7b73619c730de2169bfccb13008ed2f8afe9 bbf4620447bf052bd40435fd1f541030658fd129 c6cf1fc45077ed479d854a80a0ede0eda457e18c fe9d6c8e46fcde5a67847fe1d1e48dbb4791f001" -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/wise/dbgsym-root/DEBIAN/control dpkg-gencontrol -pwise -ldebian/changelog -Tdebian/wise.substvars -Pdebian/wise chmod 0644 -- debian/wise/DEBIAN/control dh_md5sums -a install -m0755 -d debian/wise/DEBIAN cd debian/wise >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/wise/DEBIAN/md5sums install -m0755 -d debian/.debhelper/wise/dbgsym-root/DEBIAN cd debian/.debhelper/wise/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/.debhelper/wise/dbgsym-root/DEBIAN/md5sums dh_builddeb -a dpkg-deb --root-owner-group --build debian/wise .. dpkg-deb: building package 'wise' in '../wise_2.4.1-23_arm64.deb'. dpkg-deb --root-owner-group --build debian/.debhelper/wise/dbgsym-root .. dpkg-deb: building package 'wise-dbgsym' in '../wise-dbgsym_2.4.1-23_arm64.deb'. dpkg-genbuildinfo --build=any -O../wise_2.4.1-23_arm64.buildinfo dpkg-genchanges --build=any -O../wise_2.4.1-23_arm64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2024-01-07T00:57:28Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ wise_2.4.1-23_arm64.changes: ---------------------------- Format: 1.8 Date: Sat, 18 Apr 2020 17:57:01 +0200 Source: wise Binary: wise wise-dbgsym Built-For-Profiles: cross nocheck Architecture: arm64 Version: 2.4.1-23 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Helmut Grohne Description: wise - comparison of biopolymers, like DNA and protein sequences Closes: 958094 Changes: wise (2.4.1-23) unstable; urgency=medium . * Team upload. * Do not hard code the build architecture pkg-config Closes: #958094 Checksums-Sha1: 0e81adca7261c6b4e54d79401caa46a402def5c1 8142340 wise-dbgsym_2.4.1-23_arm64.deb f65709dc26e66387cf334eccbfcc5e4427b672ef 10030 wise_2.4.1-23_arm64.buildinfo 2d3b3a086cb591911272c35307739ec79293c94c 1017980 wise_2.4.1-23_arm64.deb Checksums-Sha256: 0480f64cc9b66b3ef1ff5b9e2154088b232293620088b63db983e663efb7110e 8142340 wise-dbgsym_2.4.1-23_arm64.deb 4db2da23d3f63a7b8fb9215c996a158fbd01e609d8e477855301cee7e606acd2 10030 wise_2.4.1-23_arm64.buildinfo 62ffc837450279e7354b41ba746d60f11bd6b5fdd07bae808c2e06bf86b484c0 1017980 wise_2.4.1-23_arm64.deb Files: 7447b469f4ff86f7eb4a1820cbd9794e 8142340 debug optional wise-dbgsym_2.4.1-23_arm64.deb e2ea1a15de76e393e40d44dfb3f9092f 10030 science optional wise_2.4.1-23_arm64.buildinfo 691b1c67e310fd4dfaf0406b9545d749 1017980 science optional wise_2.4.1-23_arm64.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: wise Binary: wise wise-dbgsym Architecture: arm64 Version: 2.4.1-23 Checksums-Md5: 7447b469f4ff86f7eb4a1820cbd9794e 8142340 wise-dbgsym_2.4.1-23_arm64.deb 691b1c67e310fd4dfaf0406b9545d749 1017980 wise_2.4.1-23_arm64.deb Checksums-Sha1: 0e81adca7261c6b4e54d79401caa46a402def5c1 8142340 wise-dbgsym_2.4.1-23_arm64.deb 2d3b3a086cb591911272c35307739ec79293c94c 1017980 wise_2.4.1-23_arm64.deb Checksums-Sha256: 0480f64cc9b66b3ef1ff5b9e2154088b232293620088b63db983e663efb7110e 8142340 wise-dbgsym_2.4.1-23_arm64.deb 62ffc837450279e7354b41ba746d60f11bd6b5fdd07bae808c2e06bf86b484c0 1017980 wise_2.4.1-23_arm64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sun, 07 Jan 2024 00:57:28 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-14), autotools-dev (= 20220109.1), base-files (= 13), base-passwd (= 3.6.3), bash (= 5.2.21-2), binutils (= 2.41.50.20231227-1), binutils-common (= 2.41.50.20231227-1), binutils-x86-64-linux-gnu (= 2.41.50.20231227-1), bsdextrautils (= 2.39.3-6), bsdutils (= 1:2.39.3-6), build-essential (= 12.10), bzip2 (= 1.0.8-5+b2), coreutils (= 9.4-3), cpp (= 4:13.2.0-2), cpp-11 (= 11.4.0-7), cpp-13 (= 13.2.0-9), dash (= 0.5.12-6), debconf (= 1.5.83), debhelper (= 13.11.9), debianutils (= 5.16), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.10-1), docbook (= 4.5-10), docbook-to-man (= 1:2.0.0-45), dpkg (= 1.22.2), dpkg-dev (= 1.22.2), dwz (= 0.15-1), file (= 1:5.45-2+b1), findutils (= 4.9.0-5), fontconfig-config (= 2.14.2-6+b1), fonts-dejavu-core (= 2.37-8), fonts-dejavu-mono (= 2.37-8), fonts-lmodern (= 2.005-1), fonts-urw-base35 (= 20200910-7), g++ (= 4:13.2.0-2), g++-13 (= 13.2.0-9), gcc (= 4:13.2.0-2), gcc-11 (= 11.4.0-7), gcc-11-base (= 11.4.0-7), gcc-13 (= 13.2.0-9), gcc-13-base (= 13.2.0-9), gettext (= 0.21-14), gettext-base (= 0.21-14), ghostscript (= 10.02.1~dfsg-2), grep (= 3.11-4), groff-base (= 1.23.0-3), gzip (= 1.12-1), hevea (= 2.36-2+b1), hicolor-icon-theme (= 0.17-2), hostname (= 3.23+nmu1), imagemagick (= 8:6.9.12.98+dfsg1-5), imagemagick-6-common (= 8:6.9.12.98+dfsg1-5), imagemagick-6.q16 (= 8:6.9.12.98+dfsg1-5), init-system-helpers (= 1.66), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.1-4), libarchive-zip-perl (= 1.68-1), libasan6 (= 11.4.0-7), libasan8 (= 13.2.0-9), libatomic1 (= 13.2.0-9), libattr1 (= 1:2.5.1-5), libaudit-common (= 1:3.1.2-1), libaudit1 (= 1:3.1.2-1), libavahi-client3 (= 0.8-13+b1), libavahi-common-data (= 0.8-13+b1), libavahi-common3 (= 0.8-13+b1), libbinutils (= 2.41.50.20231227-1), libblkid-dev (= 2.39.3-6), libblkid1 (= 2.39.3-6), libbrotli1 (= 1.1.0-2+b3), libbsd0 (= 0.11.7-4), libbz2-1.0 (= 1.0.8-5+b2), libc-bin (= 2.37-13), libc-dev-bin (= 2.37-13), libc6 (= 2.37-13), libc6-dev (= 2.37-13), libcairo2 (= 1.18.0-1+b1), libcap-ng0 (= 0.8.4-1), libcap2 (= 1:2.66-4+b2), libcc1-0 (= 13.2.0-9), libcom-err2 (= 1.47.0-2+b1), libcrypt-dev (= 1:4.4.36-4), libcrypt1 (= 1:4.4.36-4), libctf-nobfd0 (= 2.41.50.20231227-1), libctf0 (= 2.41.50.20231227-1), libcups2 (= 2.4.7-1+b1), libdatrie1 (= 0.2.13-3), libdav1d7 (= 1.3.0-2+b1), libdb5.3 (= 5.3.28+dfsg2-4+b1), libdbus-1-3 (= 1.14.10-3+b1), libde265-0 (= 1.0.15-1), libdebconfclient0 (= 0.271), libdebhelper-perl (= 13.11.9), libdeflate0 (= 1.18-1), libdpkg-perl (= 1.22.2), libelf1 (= 0.190-1+b1), libexpat1 (= 2.5.0-2+b2), libffi-dev (= 3.4.4-2), libffi8 (= 3.4.4-2), libfftw3-double3 (= 3.3.10-1), libfile-find-rule-perl (= 0.34-3), libfile-homedir-perl (= 1.006-2), libfile-stripnondeterminism-perl (= 1.13.1-1), libfile-which-perl (= 1.27-2), libfontconfig1 (= 2.14.2-6+b1), libfontenc1 (= 1:1.1.4-1+b2), libfreetype6 (= 2.13.2+dfsg-1+b1), libgcc-11-dev (= 11.4.0-7), libgcc-13-dev (= 13.2.0-9), libgcc-s1 (= 13.2.0-9), libgcrypt20 (= 1.10.3-2), libgdbm-compat4 (= 1.23-5), libgdbm6 (= 1.23-5), libglib2.0-0 (= 2.78.3-1), libglib2.0-bin (= 2.78.3-1), libglib2.0-data (= 2.78.3-1), libglib2.0-dev (= 2.78.3-1), libglib2.0-dev-bin (= 2.78.3-1), libgmp10 (= 2:6.3.0+dfsg-2), libgnutls30 (= 3.8.2-1), libgomp1 (= 13.2.0-9), libgpg-error0 (= 1.47-3), libgprofng0 (= 2.41.50.20231227-1), libgraphite2-3 (= 1.3.14-2), libgs-common (= 10.02.1~dfsg-2), libgs10 (= 10.02.1~dfsg-2), libgs10-common (= 10.02.1~dfsg-2), libgssapi-krb5-2 (= 1.20.1-5), libharfbuzz0b (= 8.0.1-1+b2), libheif-plugin-dav1d (= 1.17.6-1), libheif-plugin-libde265 (= 1.17.6-1), libheif1 (= 1.17.6-1), libhogweed6 (= 3.9.1-2), libhwasan0 (= 13.2.0-9), libice6 (= 2:1.0.10-1), libicu72 (= 72.1-4), libidn12 (= 1.41-1), libidn2-0 (= 2.3.4-1+b2), libijs-0.35 (= 0.35-15.1), libisl23 (= 0.26-3+b2), libitm1 (= 13.2.0-9), libjansson4 (= 2.14-2+b2), libjbig0 (= 2.1-6.1), libjbig2dec0 (= 0.20-1), libjpeg62-turbo (= 1:2.1.5-2+b2), libjs-jquery (= 3.6.1+dfsg+~3.5.14-1), libk5crypto3 (= 1.20.1-5), libkeyutils1 (= 1.6.3-2+b2), libkpathsea6 (= 2023.20230311.66589-8), libkrb5-3 (= 1.20.1-5), libkrb5support0 (= 1.20.1-5), liblcms2-2 (= 2.14-2), liblerc4 (= 4.0.0+ds-4), liblqr-1-0 (= 0.4.2-2.1), liblsan0 (= 13.2.0-9), libltdl7 (= 2.4.7-7), liblz4-1 (= 1.9.4-1+b2), liblzma5 (= 5.4.5-0.3), libmagic-mgc (= 1:5.45-2+b1), libmagic1 (= 1:5.45-2+b1), libmagickcore-6.q16-7 (= 8:6.9.12.98+dfsg1-5), libmagickwand-6.q16-7 (= 8:6.9.12.98+dfsg1-5), libmd0 (= 1.1.0-2), libmime-charset-perl (= 1.013.1-2), libmount-dev (= 2.39.3-6), libmount1 (= 2.39.3-6), libmpc3 (= 1.3.1-1+b2), libmpfr6 (= 4.2.1-1), libncursesw6 (= 6.4+20231209-1), libnetpbm11 (= 2:11.04.05-2), libnettle8 (= 3.9.1-2), libnsl-dev (= 1.3.0-3), libnsl2 (= 1.3.0-3), libnumber-compare-perl (= 0.03-3), libopenjp2-7 (= 2.5.0-2+b2), libosp5 (= 1.5.2-14), libp11-kit0 (= 0.25.3-4), libpam-modules (= 1.5.2-9.1+b1), libpam-modules-bin (= 1.5.2-9.1+b1), libpam-runtime (= 1.5.2-9.1), libpam0g (= 1.5.2-9.1+b1), libpaper-utils (= 1.1.29), libpaper1 (= 1.1.29), libpcre2-16-0 (= 10.42-4), libpcre2-32-0 (= 10.42-4), libpcre2-8-0 (= 10.42-4), libpcre2-dev (= 10.42-4), libpcre2-posix3 (= 10.42-4), libperl5.36 (= 5.36.0-10+b1), libpipeline1 (= 1.5.7-1+b2), libpixman-1-0 (= 0.42.2-1), libpkgconf3 (= 1.8.1-1+b2), libpng16-16 (= 1.6.40-3), libpotrace0 (= 1.16-2), libptexenc1 (= 2023.20230311.66589-8), libpython3-stdlib (= 3.11.6-1), libpython3.11-minimal (= 3.11.7-2), libpython3.11-stdlib (= 3.11.7-2), libquadmath0 (= 13.2.0-9), libraw23 (= 0.21.1-7), libreadline8 (= 8.2-3), libseccomp2 (= 2.5.5-1), libselinux1 (= 3.5-1+b2), libselinux1-dev (= 3.5-1+b2), libsepol-dev (= 3.5-2), libsepol2 (= 3.5-2), libsframe1 (= 2.41.50.20231227-1), libsharpyuv0 (= 1.3.2-0.3), libsm6 (= 2:1.2.3-1), libsmartcols1 (= 2.39.3-6), libsombok3 (= 2.4.0-2+b1), libsqlite3-0 (= 3.44.2-1), libssl3 (= 3.1.4-2), libstdc++-13-dev (= 13.2.0-9), libstdc++6 (= 13.2.0-9), libsub-override-perl (= 0.10-1), libsynctex2 (= 2023.20230311.66589-8), libsystemd0 (= 255.2-4), libtasn1-6 (= 4.19.0-3+b2), libteckit0 (= 2.5.11+ds1-1+b1), libtexlua53-5 (= 2023.20230311.66589-8), libtext-glob-perl (= 0.11-3), libthai-data (= 0.1.29-2), libthai0 (= 0.1.29-2), libtiff6 (= 4.5.1+git230720-3), libtinfo6 (= 6.4+20231209-1), libtirpc-common (= 1.3.4+ds-1), libtirpc-dev (= 1.3.4+ds-1), libtirpc3 (= 1.3.4+ds-1), libtool (= 2.4.7-7), libtsan0 (= 11.4.0-7), libtsan2 (= 13.2.0-9), libubsan1 (= 13.2.0-9), libuchardet0 (= 0.0.8-1), libudev1 (= 255.2-4), libunicode-linebreak-perl (= 0.0.20190101-1+b5), libunistring5 (= 1.1-2), libuuid1 (= 2.39.3-6), libwebp7 (= 1.3.2-0.3), libwebpdemux2 (= 1.3.2-0.3), libwebpmux3 (= 1.3.2-0.3), libx11-6 (= 2:1.8.7-1), libx11-data (= 2:1.8.7-1), libxau6 (= 1:1.0.9-1), libxaw7 (= 2:1.0.14-1), libxcb-render0 (= 1.15-1), libxcb-shm0 (= 1.15-1), libxcb1 (= 1.15-1), libxdmcp6 (= 1:1.1.2-3), libxext6 (= 2:1.3.4-1+b1), libxi6 (= 2:1.8-1+b1), libxml2 (= 2.9.14+dfsg-1.3+b2), libxmu6 (= 2:1.1.3-3), libxpm4 (= 1:3.5.17-1), libxrender1 (= 1:0.9.10-1.1), libxt6 (= 1:1.2.1-1.1), libyaml-tiny-perl (= 1.74-1), libzstd1 (= 1.5.5+dfsg2-2), libzzip-0-13 (= 0.13.72+dfsg.1-1.1), linux-libc-dev (= 6.6.9-1), lmodern (= 2.005-1), login (= 1:4.13+dfsg1-3+b1), m4 (= 1.4.19-4), make (= 4.3-4.1), man-db (= 2.12.0-1), mawk (= 1.3.4.20231126-1), media-types (= 10.1.0), ncurses-base (= 6.4+20231209-1), ncurses-bin (= 6.4+20231209-1), netbase (= 6.4), netpbm (= 2:11.04.05-2), opensp (= 1.5.2-14), patch (= 2.7.6-7), perl (= 5.36.0-10+b1), perl-base (= 5.36.0-10+b1), perl-modules-5.36 (= 5.36.0-10), pkg-config (= 1.8.1-1+b2), pkgconf (= 1.8.1-1+b2), pkgconf-bin (= 1.8.1-1+b2), po-debconf (= 1.0.21+nmu1), poppler-data (= 0.4.12-1), python3 (= 3.11.6-1), python3-distutils (= 3.11.5-1), python3-lib2to3 (= 3.11.5-1), python3-minimal (= 3.11.6-1), python3.11 (= 3.11.7-2), python3.11-minimal (= 3.11.7-2), readline-common (= 8.2-3), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.20), sgml-base (= 1.31), sgml-data (= 2.0.11+nmu1), sysvinit-utils (= 3.08-5), t1utils (= 1.41-4), tar (= 1.35+dfsg-2), tex-common (= 6.18), texlive-base (= 2023.20231207-1), texlive-binaries (= 2023.20230311.66589-8), texlive-extra-utils (= 2023.20231207-3), texlive-latex-base (= 2023.20231207-1), texlive-luatex (= 2023.20231207-1), texlive-plain-generic (= 2023.20231207-3), tzdata (= 2023d-1), ucf (= 3.0043+nmu1), usrmerge (= 38), util-linux (= 2.39.3-6), uuid-dev (= 2.39.3-6), x11-common (= 1:7.7+23), xdg-utils (= 1.1.3-4.1), xfonts-encodings (= 1:1.0.4-2.2), xfonts-utils (= 1:7.7+6), xml-core (= 0.19), xz-utils (= 5.4.5-0.3), zlib1g (= 1:1.3.dfsg-3), zlib1g-dev (= 1:1.3.dfsg-3) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_US.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1587225421" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ wise-dbgsym_2.4.1-23_arm64.deb ------------------------------ new Debian package, version 2.0. size 8142340 bytes: control archive=1136 bytes. 812 bytes, 12 lines control 1354 bytes, 13 lines md5sums Package: wise-dbgsym Source: wise Version: 2.4.1-23 Auto-Built-Package: debug-symbols Architecture: arm64 Maintainer: Debian Med Packaging Team Installed-Size: 9438 Depends: wise (= 2.4.1-23) Section: debug Priority: optional Description: debug symbols for wise Build-Ids: 14410329288faccb18fe258e9d1249dc468e120e 15b1e39bfe0c57dc068f60bd18f0f10b411b4033 17a3e050be221b68cab21de6f8e5f9284cac0f35 29cff3c402d3391f7ba45081fa4ae7f8c97bdcdd 4b4bc36b0b0ea0723103707527196f9dd48d4dc7 7469eedc1e1e9bdc30266552ad7494daf21fe612 7cba31a03f4c94c0a7360127dd506126170a654b 80ef38b40ad409f83410a468630df328bd41c3fd 8aac7b73619c730de2169bfccb13008ed2f8afe9 bbf4620447bf052bd40435fd1f541030658fd129 c6cf1fc45077ed479d854a80a0ede0eda457e18c fe9d6c8e46fcde5a67847fe1d1e48dbb4791f001 drwxr-xr-x root/root 0 2020-04-18 15:57 ./ drwxr-xr-x root/root 0 2020-04-18 15:57 ./usr/ drwxr-xr-x root/root 0 2020-04-18 15:57 ./usr/lib/ drwxr-xr-x root/root 0 2020-04-18 15:57 ./usr/lib/debug/ drwxr-xr-x root/root 0 2020-04-18 15:57 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2020-04-18 15:57 ./usr/lib/debug/.build-id/14/ -rw-r--r-- root/root 244648 2020-04-18 15:57 ./usr/lib/debug/.build-id/14/410329288faccb18fe258e9d1249dc468e120e.debug drwxr-xr-x root/root 0 2020-04-18 15:57 ./usr/lib/debug/.build-id/15/ -rw-r--r-- root/root 1661688 2020-04-18 15:57 ./usr/lib/debug/.build-id/15/b1e39bfe0c57dc068f60bd18f0f10b411b4033.debug drwxr-xr-x root/root 0 2020-04-18 15:57 ./usr/lib/debug/.build-id/17/ -rw-r--r-- root/root 252920 2020-04-18 15:57 ./usr/lib/debug/.build-id/17/a3e050be221b68cab21de6f8e5f9284cac0f35.debug drwxr-xr-x root/root 0 2020-04-18 15:57 ./usr/lib/debug/.build-id/29/ -rw-r--r-- root/root 1656232 2020-04-18 15:57 ./usr/lib/debug/.build-id/29/cff3c402d3391f7ba45081fa4ae7f8c97bdcdd.debug drwxr-xr-x root/root 0 2020-04-18 15:57 ./usr/lib/debug/.build-id/4b/ -rw-r--r-- root/root 370744 2020-04-18 15:57 ./usr/lib/debug/.build-id/4b/4bc36b0b0ea0723103707527196f9dd48d4dc7.debug drwxr-xr-x root/root 0 2020-04-18 15:57 ./usr/lib/debug/.build-id/74/ -rw-r--r-- root/root 353296 2020-04-18 15:57 ./usr/lib/debug/.build-id/74/69eedc1e1e9bdc30266552ad7494daf21fe612.debug drwxr-xr-x root/root 0 2020-04-18 15:57 ./usr/lib/debug/.build-id/7c/ -rw-r--r-- root/root 433272 2020-04-18 15:57 ./usr/lib/debug/.build-id/7c/ba31a03f4c94c0a7360127dd506126170a654b.debug drwxr-xr-x root/root 0 2020-04-18 15:57 ./usr/lib/debug/.build-id/80/ -rw-r--r-- root/root 543016 2020-04-18 15:57 ./usr/lib/debug/.build-id/80/ef38b40ad409f83410a468630df328bd41c3fd.debug drwxr-xr-x root/root 0 2020-04-18 15:57 ./usr/lib/debug/.build-id/8a/ -rw-r--r-- root/root 1665744 2020-04-18 15:57 ./usr/lib/debug/.build-id/8a/ac7b73619c730de2169bfccb13008ed2f8afe9.debug drwxr-xr-x root/root 0 2020-04-18 15:57 ./usr/lib/debug/.build-id/bb/ -rw-r--r-- root/root 349048 2020-04-18 15:57 ./usr/lib/debug/.build-id/bb/f4620447bf052bd40435fd1f541030658fd129.debug drwxr-xr-x root/root 0 2020-04-18 15:57 ./usr/lib/debug/.build-id/c6/ -rw-r--r-- root/root 342048 2020-04-18 15:57 ./usr/lib/debug/.build-id/c6/cf1fc45077ed479d854a80a0ede0eda457e18c.debug drwxr-xr-x root/root 0 2020-04-18 15:57 ./usr/lib/debug/.build-id/fe/ -rw-r--r-- root/root 1661672 2020-04-18 15:57 ./usr/lib/debug/.build-id/fe/9d6c8e46fcde5a67847fe1d1e48dbb4791f001.debug drwxr-xr-x root/root 0 2020-04-18 15:57 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2020-04-18 15:57 ./usr/lib/debug/.dwz/aarch64-linux-gnu/ -rw-r--r-- root/root 99816 2020-04-18 15:57 ./usr/lib/debug/.dwz/aarch64-linux-gnu/wise.debug drwxr-xr-x root/root 0 2020-04-18 15:57 ./usr/share/ drwxr-xr-x root/root 0 2020-04-18 15:57 ./usr/share/doc/ lrwxrwxrwx root/root 0 2020-04-18 15:57 ./usr/share/doc/wise-dbgsym -> wise wise_2.4.1-23_arm64.deb ----------------------- new Debian package, version 2.0. size 1017980 bytes: control archive=1964 bytes. 1721 bytes, 33 lines control 1742 bytes, 29 lines md5sums Package: wise Version: 2.4.1-23 Architecture: arm64 Maintainer: Debian Med Packaging Team Installed-Size: 10187 Depends: libc6 (>= 2.34), libglib2.0-0 (>= 2.12.0), wise-data (= 2.4.1-23) Suggests: wise-doc (= 2.4.1-23) Section: science Priority: optional Homepage: https://www.ebi.ac.uk/~birney/wise2/ Description: comparison of biopolymers, like DNA and protein sequences Wise2 is a package focused on comparisons of biopolymers, commonly DNA and protein sequences. There are many other packages which do this, probably the best known being BLAST package (from NCBI) and the Fasta package (from Bill Pearson). There are other packages, such as the HMMER package (Sean Eddy) or SAM package (UC Santa Cruz) focused on hidden Markov models (HMMs) of biopolymers. . Wise2's particular forte is the comparison of DNA sequence at the level of its protein translation. This comparison allows the simultaneous prediction of say gene structure with homology based alignment. . Wise2 also contains other algorithms, such as the venerable Smith-Waterman algorithm, or more modern ones such as Stephen Altschul's generalised gap penalties, or even experimental ones developed in house, such as dba. The development of these algorithms is due to the ease of developing such algorithms in the environment used by Wise2. . Wise2 has also been written with an eye for reuse and maintainability. Although it is a pure C package you can access its functionality directly in Perl. Parts of the package (or the entire package) can be used by other C or C++ programs without namespace clashes as all externally linked variables have the unique identifier Wise2 prepended. drwxr-xr-x root/root 0 2020-04-18 15:57 ./ drwxr-xr-x root/root 0 2020-04-18 15:57 ./usr/ drwxr-xr-x root/root 0 2020-04-18 15:57 ./usr/bin/ -rwxr-xr-x root/root 329952 2020-04-18 15:57 ./usr/bin/dba -rwxr-xr-x root/root 264352 2020-04-18 15:57 ./usr/bin/dnal -rwxr-xr-x root/root 1839376 2020-04-18 15:57 ./usr/bin/estwise -rwxr-xr-x root/root 1839488 2020-04-18 15:57 ./usr/bin/estwisedb -rwxr-xr-x root/root 1839472 2020-04-18 15:57 ./usr/bin/genewise -rwxr-xr-x root/root 1839552 2020-04-18 15:57 ./usr/bin/genewisedb -rwxr-xr-x root/root 395384 2020-04-18 15:57 ./usr/bin/genomewise -rwxr-xr-x root/root 460960 2020-04-18 15:57 ./usr/bin/promoterwise -rwxr-xr-x root/root 395424 2020-04-18 15:57 ./usr/bin/psw -rwxr-xr-x root/root 395504 2020-04-18 15:57 ./usr/bin/pswdb -rwxr-xr-x root/root 526496 2020-04-18 15:57 ./usr/bin/scanwise -rwxr-xr-x root/root 264336 2020-04-18 15:57 ./usr/bin/scanwise_server drwxr-xr-x root/root 0 2020-04-18 15:57 ./usr/share/ drwxr-xr-x root/root 0 2020-04-18 15:57 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-04-18 15:57 ./usr/share/doc/wise/ -rw-r--r-- root/root 1973 2007-07-01 20:46 ./usr/share/doc/wise/README -rw-r--r-- root/root 320 2020-04-18 15:57 ./usr/share/doc/wise/README.Debian -rw-r--r-- root/root 912 2020-04-18 15:57 ./usr/share/doc/wise/changelog.Debian.gz -rw-r--r-- root/root 4297 2020-04-18 15:57 ./usr/share/doc/wise/copyright -rw-r--r-- root/root 312 2020-04-18 15:57 ./usr/share/doc/wise/run-unit-test drwxr-xr-x root/root 0 2020-04-18 15:57 ./usr/share/man/ drwxr-xr-x root/root 0 2020-04-18 15:57 ./usr/share/man/man1/ -rw-r--r-- root/root 846 2020-04-18 15:57 ./usr/share/man/man1/dba.1.gz -rw-r--r-- root/root 557 2020-04-18 15:57 ./usr/share/man/man1/dnal.1.gz -rw-r--r-- root/root 595 2020-04-18 15:57 ./usr/share/man/man1/estwise.1.gz -rw-r--r-- root/root 594 2020-04-18 15:57 ./usr/share/man/man1/estwisedb.1.gz -rw-r--r-- root/root 594 2020-04-18 15:57 ./usr/share/man/man1/genewise.1.gz -rw-r--r-- root/root 595 2020-04-18 15:57 ./usr/share/man/man1/genewisedb.1.gz -rw-r--r-- root/root 605 2020-04-18 15:57 ./usr/share/man/man1/genomewise.1.gz -rw-r--r-- root/root 592 2020-04-18 15:57 ./usr/share/man/man1/promoterwise.1.gz -rw-r--r-- root/root 685 2020-04-18 15:57 ./usr/share/man/man1/psw.1.gz -rw-r--r-- root/root 585 2020-04-18 15:57 ./usr/share/man/man1/pswdb.1.gz -rw-r--r-- root/root 601 2020-04-18 15:57 ./usr/share/man/man1/scanwise.1.gz -rw-r--r-- root/root 584 2020-04-18 15:57 ./usr/share/man/man1/scanwise_server.1.gz lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:amd64 Filtered Build-Depends: lintian:amd64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/apt_archive/sbuild-build-depends-lintian-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [615 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [1376 B] Get:5 copy:/<>/apt_archive ./ Packages [1455 B] Fetched 3446 B in 0s (0 B/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... Execute external solver... The following additional packages will be installed: ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libfile-basedir-perl libfile-listing-perl libfont-ttf-perl libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-someutils-perl liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libterm-readkey-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl libwww-robotrules-perl libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop openssl patchutils perl-openssl-defaults plzip unzip Suggested packages: isoquery libxml-parser-perl libdata-dump-perl libcrypt-ssleay-perl libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libbusiness-isbn-perl libregexp-ipv6-perl libauthen-ntlm-perl binutils-multiarch libtext-template-perl zip Recommended packages: gnupg libcgi-fast-perl libhtml-format-perl libio-compress-brotli-perl liblist-someutils-xs-perl libfreezethaw-perl libmath-base85-perl libsocket6-perl libpackage-stash-xs-perl libxstring-perl libdata-dump-perl libhttp-daemon-perl libmailtools-perl The following NEW packages will be installed: ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libfile-basedir-perl libfile-listing-perl libfont-ttf-perl libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-someutils-perl liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libterm-readkey-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl libwww-robotrules-perl libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop openssl patchutils perl-openssl-defaults plzip sbuild-build-depends-lintian-dummy:arm64 unzip 0 upgraded, 121 newly installed, 0 to remove and 0 not upgraded. Need to get 12.6 MB of archives. After this operation, 48.7 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [856 B] Get:2 http://localhost:3142/debian sid/main amd64 openssl amd64 3.1.4-2 [1426 kB] Get:3 http://localhost:3142/debian sid/main amd64 ca-certificates all 20230311 [153 kB] Get:4 http://localhost:3142/debian sid/main amd64 diffstat amd64 1.65-1 [33.3 kB] Get:5 http://localhost:3142/debian sid/main amd64 libassuan0 amd64 2.5.6-1 [49.9 kB] Get:6 http://localhost:3142/debian sid/main amd64 gpgconf amd64 2.2.40-1.1 [564 kB] Get:7 http://localhost:3142/debian sid/main amd64 gpg amd64 2.2.40-1.1 [949 kB] Get:8 http://localhost:3142/debian sid/main amd64 iso-codes all 4.15.0-1 [2906 kB] Get:9 http://localhost:3142/debian sid/main amd64 libaliased-perl all 0.34-3 [13.5 kB] Get:10 http://localhost:3142/debian sid/main amd64 libapt-pkg-perl amd64 0.1.40+b2 [69.2 kB] Get:11 http://localhost:3142/debian sid/main amd64 libb-hooks-op-check-perl amd64 0.22-2+b1 [10.5 kB] Get:12 http://localhost:3142/debian sid/main 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libcapture-tiny-perl all 0.48-2 [24.6 kB] Get:23 http://localhost:3142/debian sid/main amd64 libhtml-tagset-perl all 3.20-6 [11.7 kB] Get:24 http://localhost:3142/debian sid/main amd64 liburi-perl all 5.21-1 [95.6 kB] Get:25 http://localhost:3142/debian sid/main amd64 libhtml-parser-perl amd64 3.81-1 [101 kB] Get:26 http://localhost:3142/debian sid/main amd64 libcgi-pm-perl all 4.60-1 [219 kB] Get:27 http://localhost:3142/debian sid/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get:28 http://localhost:3142/debian sid/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get:29 http://localhost:3142/debian sid/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b1 [36.4 kB] Get:30 http://localhost:3142/debian sid/main amd64 libclone-perl amd64 0.46-1 [13.7 kB] Get:31 http://localhost:3142/debian sid/main amd64 libconfig-tiny-perl all 2.30-1 [18.9 kB] Get:32 http://localhost:3142/debian sid/main amd64 libparams-util-perl amd64 1.102-2+b1 [24.8 kB] Get:33 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libdata-messagepack-perl amd64 1.02-1+b1 [35.2 kB] Get:44 http://localhost:3142/debian sid/main amd64 libnet-domain-tld-perl all 1.75-3 [31.9 kB] Get:45 http://localhost:3142/debian sid/main amd64 libdata-validate-domain-perl all 0.10-1.1 [11.1 kB] Get:46 http://localhost:3142/debian sid/main amd64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB] Get:47 http://localhost:3142/debian sid/main amd64 libnet-netmask-perl all 2.0002-2 [28.6 kB] Get:48 http://localhost:3142/debian sid/main amd64 libnetaddr-ip-perl amd64 4.079+dfsg-2+b1 [99.5 kB] Get:49 http://localhost:3142/debian sid/main amd64 libdata-validate-ip-perl all 0.31-1 [20.6 kB] Get:50 http://localhost:3142/debian sid/main amd64 libdata-validate-uri-perl all 0.07-2 [11.2 kB] Get:51 http://localhost:3142/debian sid/main amd64 libdevel-size-perl amd64 0.83-2+b1 [24.3 kB] Get:52 http://localhost:3142/debian sid/main amd64 libemail-address-xs-perl amd64 1.05-1+b1 [29.4 kB] Get:53 http://localhost:3142/debian sid/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get:54 http://localhost:3142/debian sid/main amd64 libipc-system-simple-perl all 1.30-2 [26.8 kB] Get:55 http://localhost:3142/debian sid/main amd64 libfile-basedir-perl all 0.09-2 [15.1 kB] Get:56 http://localhost:3142/debian sid/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:57 http://localhost:3142/debian sid/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get:58 http://localhost:3142/debian sid/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get:59 http://localhost:3142/debian sid/main amd64 libfont-ttf-perl all 1.06-2 [318 kB] Get:60 http://localhost:3142/debian sid/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get:61 http://localhost:3142/debian sid/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get:62 http://localhost:3142/debian sid/main amd64 libhttp-message-perl all 6.45-1 [82.0 kB] Get:63 http://localhost:3142/debian sid/main amd64 libhtml-form-perl all 6.11-1 [33.1 kB] Get:64 http://localhost:3142/debian sid/main amd64 libhtml-html5-entities-perl all 0.004-3 [21.0 kB] Get:65 http://localhost:3142/debian sid/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get:66 http://localhost:3142/debian sid/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get:67 http://localhost:3142/debian sid/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get:68 http://localhost:3142/debian sid/main amd64 perl-openssl-defaults amd64 7+b1 [7924 B] Get:69 http://localhost:3142/debian sid/main amd64 libnet-ssleay-perl amd64 1.92-2+b1 [317 kB] Get:70 http://localhost:3142/debian sid/main amd64 libio-socket-ssl-perl all 2.084-1 [216 kB] Get:71 http://localhost:3142/debian sid/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get:72 http://localhost:3142/debian sid/main amd64 liblwp-protocol-https-perl all 6.11-1 [10.5 kB] Get:73 http://localhost:3142/debian sid/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:74 http://localhost:3142/debian sid/main amd64 libwww-perl all 6.72-1 [187 kB] Get:75 http://localhost:3142/debian sid/main amd64 libhtml-tokeparser-simple-perl all 3.16-4 [39.1 kB] Get:76 http://localhost:3142/debian sid/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get:77 http://localhost:3142/debian sid/main amd64 libio-interactive-perl all 1.025-1 [11.4 kB] Get:78 http://localhost:3142/debian sid/main amd64 libipc-run3-perl all 0.048-3 [33.2 kB] Get:79 http://localhost:3142/debian sid/main amd64 libjson-maybexs-perl all 1.004005-1 [12.9 kB] Get:80 http://localhost:3142/debian sid/main amd64 liblist-compare-perl all 0.55-2 [65.7 kB] Get:81 http://localhost:3142/debian sid/main amd64 liblist-someutils-perl all 0.59-1 [37.1 kB] Get:82 http://localhost:3142/debian sid/main amd64 liblist-utilsby-perl all 0.12-2 [15.5 kB] Get:83 http://localhost:3142/debian sid/main amd64 liblz1 amd64 1.13-6 [37.8 kB] Get:84 http://localhost:3142/debian sid/main amd64 liblzo2-2 amd64 2.10-2 [56.9 kB] Get:85 http://localhost:3142/debian sid/main amd64 libmarkdown2 amd64 2.2.7-2+b1 [35.6 kB] Get:86 http://localhost:3142/debian sid/main amd64 libmldbm-perl all 2.05-4 [16.8 kB] Get:87 http://localhost:3142/debian sid/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get:88 http://localhost:3142/debian sid/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get:89 http://localhost:3142/debian sid/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get:90 http://localhost:3142/debian sid/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:91 http://localhost:3142/debian sid/main amd64 libmoox-aliases-perl all 0.001006-2 [7156 B] Get:92 http://localhost:3142/debian sid/main amd64 libmouse-perl amd64 2.5.10-1+b3 [170 kB] Get:93 http://localhost:3142/debian sid/main amd64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get:94 http://localhost:3142/debian sid/main amd64 libsub-identify-perl amd64 0.14-3 [10.9 kB] Get:95 http://localhost:3142/debian sid/main amd64 libsub-name-perl amd64 0.27-1 [12.5 kB] Get:96 http://localhost:3142/debian sid/main amd64 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get:97 http://localhost:3142/debian sid/main amd64 libpath-tiny-perl all 0.144-1 [56.4 kB] Get:98 http://localhost:3142/debian sid/main amd64 libperlio-gzip-perl amd64 0.20-1+b1 [17.3 kB] Get:99 http://localhost:3142/debian sid/main amd64 libperlio-utf8-strict-perl amd64 0.010-1 [11.4 kB] Get:100 http://localhost:3142/debian sid/main amd64 libproc-processtable-perl amd64 0.636-1 [43.0 kB] Get:101 http://localhost:3142/debian sid/main amd64 libregexp-wildcards-perl all 1.05-3 [14.1 kB] Get:102 http://localhost:3142/debian sid/main amd64 libsereal-decoder-perl amd64 5.004+ds-1 [99.5 kB] Get:103 http://localhost:3142/debian sid/main amd64 libsereal-encoder-perl amd64 5.004+ds-1 [102 kB] Get:104 http://localhost:3142/debian sid/main amd64 libsort-versions-perl all 1.62-3 [8928 B] Get:105 http://localhost:3142/debian sid/main amd64 libxs-parse-keyword-perl amd64 0.39-1 [60.3 kB] Get:106 http://localhost:3142/debian sid/main amd64 libsyntax-keyword-try-perl amd64 0.29-1 [28.8 kB] Get:107 http://localhost:3142/debian sid/main amd64 libterm-readkey-perl amd64 2.38-2+b1 [24.5 kB] Get:108 http://localhost:3142/debian sid/main amd64 libtext-levenshteinxs-perl amd64 0.03-5+b1 [8404 B] Get:109 http://localhost:3142/debian sid/main amd64 libtext-markdown-discount-perl amd64 0.16-1 [13.0 kB] Get:110 http://localhost:3142/debian sid/main amd64 libtext-xslate-perl amd64 3.5.9-1+b2 [198 kB] Get:111 http://localhost:3142/debian sid/main amd64 libtime-duration-perl all 1.21-2 [13.1 kB] Get:112 http://localhost:3142/debian sid/main amd64 libtime-moment-perl amd64 0.44-2+b1 [73.0 kB] Get:113 http://localhost:3142/debian sid/main amd64 libunicode-utf8-perl amd64 0.62-2 [20.2 kB] Get:114 http://localhost:3142/debian sid/main amd64 libwww-mechanize-perl all 2.17-1 [116 kB] Get:115 http://localhost:3142/debian sid/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB] Get:116 http://localhost:3142/debian sid/main amd64 libyaml-libyaml-perl amd64 0.86+ds-1 [34.4 kB] Get:117 http://localhost:3142/debian sid/main amd64 plzip amd64 1.10-6 [63.1 kB] Get:118 http://localhost:3142/debian sid/main amd64 lzop amd64 1.04-2 [84.2 kB] Get:119 http://localhost:3142/debian sid/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get:120 http://localhost:3142/debian sid/main amd64 unzip amd64 6.0-28 [166 kB] Get:121 http://localhost:3142/debian sid/main amd64 lintian all 2.116.3 [1130 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 12.6 MB in 0s (99.6 MB/s) Selecting previously unselected package openssl. (Reading database ... 50093 files and directories currently installed.) Preparing to unpack .../000-openssl_3.1.4-2_amd64.deb ... Unpacking openssl (3.1.4-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../001-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package diffstat. Preparing to unpack .../002-diffstat_1.65-1_amd64.deb ... Unpacking diffstat (1.65-1) ... Selecting previously unselected package libassuan0:amd64. Preparing to unpack .../003-libassuan0_2.5.6-1_amd64.deb ... Unpacking libassuan0:amd64 (2.5.6-1) ... Selecting previously unselected package gpgconf. Preparing to unpack .../004-gpgconf_2.2.40-1.1_amd64.deb ... Unpacking gpgconf (2.2.40-1.1) ... Selecting previously unselected package gpg. Preparing to unpack .../005-gpg_2.2.40-1.1_amd64.deb ... Unpacking gpg (2.2.40-1.1) ... Selecting previously unselected package iso-codes. 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Unpacking sbuild-build-depends-lintian-dummy:arm64 (0.invalid.0) ... Setting up libapt-pkg-perl (0.1.40+b2) ... Setting up liblz1:amd64 (1.13-6) ... Setting up libberkeleydb-perl:amd64 (0.64-2+b1) ... Setting up plzip (1.10-6) ... update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip (lzip) in auto mode update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-compressor (lzip-compressor) in auto mode update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-decompressor (lzip-decompressor) in auto mode Setting up libunicode-utf8-perl (0.62-2) ... Setting up libmouse-perl (2.5.10-1+b3) ... Setting up libdata-messagepack-perl (1.02-1+b1) ... Setting up libdynaloader-functions-perl (0.003-3) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up liblist-compare-perl (0.55-2) ... Setting up libclone-perl:amd64 (0.46-1) ... Setting up libyaml-0-2:amd64 (0.2.5-1) ... Setting up libsub-identify-perl (0.14-3) ... Setting up libcpanel-json-xs-perl:amd64 (4.37-1) ... Setting up libhtml-tagset-perl (3.20-6) ... Setting up libdevel-size-perl (0.83-2+b1) ... Setting up unzip (6.0-28) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libyaml-libyaml-perl (0.86+ds-1) ... Setting up libio-interactive-perl (1.025-1) ... Setting up libtry-tiny-perl (0.31-2) ... Setting up perl-openssl-defaults:amd64 (7+b1) ... Setting up libmldbm-perl (2.05-4) ... Setting up liblzo2-2:amd64 (2.10-2) ... Setting up libtime-moment-perl (0.44-2+b1) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libassuan0:amd64 (2.5.6-1) ... Setting up libconfig-tiny-perl (2.30-1) ... Setting up libsereal-encoder-perl (5.004+ds-1) ... Setting up liblist-utilsby-perl (0.12-2) ... Setting up libnet-netmask-perl (2.0002-2) ... Setting up libsub-install-perl (0.929-1) ... Setting up patchutils (0.4.2-1) ... Setting up libjson-maybexs-perl (1.004005-1) ... Setting up libnetaddr-ip-perl (4.079+dfsg-2+b1) ... Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libxs-parse-keyword-perl (0.39-1) ... Setting up libipc-system-simple-perl (1.30-2) ... Setting up libnet-domain-tld-perl (1.75-3) ... Setting up libperlio-utf8-strict-perl (0.010-1) ... Setting up diffstat (1.65-1) ... Setting up libvariable-magic-perl (0.63-1+b1) ... Setting up libio-html-perl (1.004-3) ... Setting up libb-hooks-op-check-perl:amd64 (0.22-2+b1) ... Setting up libparams-util-perl (1.102-2+b1) ... Setting up libtime-duration-perl (1.21-2) ... Setting up libtext-xslate-perl:amd64 (3.5.9-1+b2) ... Setting up libsub-exporter-progressive-perl (0.001013-3) ... Setting up libcapture-tiny-perl (0.48-2) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libsub-name-perl:amd64 (0.27-1) ... Setting up libsyntax-keyword-try-perl (0.29-1) ... Setting up libdata-validate-domain-perl (0.10-1.1) ... Setting up libproc-processtable-perl:amd64 (0.636-1) ... Setting up libpath-tiny-perl (0.144-1) ... Setting up lzop (1.04-2) ... Setting up gpgconf (2.2.40-1.1) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libipc-run3-perl (0.048-3) ... Setting up libregexp-wildcards-perl (1.05-3) ... Setting up libaliased-perl (0.34-3) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libdevel-stacktrace-perl (2.0400-2) ... Setting up libclass-xsaccessor-perl (1.19-4+b1) ... Setting up libsort-versions-perl (1.62-3) ... Setting up libterm-readkey-perl (2.38-2+b1) ... Setting up libfont-ttf-perl (1.06-2) ... Setting up openssl (3.1.4-2) ... Setting up libtext-levenshteinxs-perl (0.03-5+b1) ... Setting up libperlio-gzip-perl (0.20-1+b1) ... Setting up libhtml-html5-entities-perl (0.004-3) ... Setting up libsereal-decoder-perl (5.004+ds-1) ... Setting up libmarkdown2:amd64 (2.2.7-2+b1) ... Setting up liburi-perl (5.21-1) ... Setting up iso-codes (4.15.0-1) ... Setting up libnet-ipv6addr-perl (1.02-1) ... Setting up gpg (2.2.40-1.1) ... Setting up libdata-validate-ip-perl (0.31-1) ... Setting up libemail-address-xs-perl (1.05-1+b1) ... Setting up libnet-ssleay-perl:amd64 (1.92-2+b1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up libfile-basedir-perl (0.09-2) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libnet-http-perl (6.23-1) ... Setting up libtext-markdown-discount-perl (0.16-1) ... Setting up libexception-class-perl (1.45-1) ... Setting up libdevel-callchecker-perl:amd64 (0.008-2) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libdata-validate-uri-perl (0.07-2) ... Setting up libdata-optlist-perl (0.114-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libhtml-parser-perl:amd64 (3.81-1) ... Setting up libio-socket-ssl-perl (2.084-1) ... Setting up libsub-exporter-perl (0.990-1) ... Setting up libhttp-message-perl (6.45-1) ... Setting up libhtml-form-perl (6.11-1) ... Setting up libiterator-perl (0.03+ds1-2) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up libiterator-util-perl (0.02+ds1-2) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libparams-classify-perl:amd64 (0.015-2+b1) ... Setting up libcgi-pm-perl (4.60-1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up libconst-fast-perl (0.014-2) ... Setting up libdata-dpath-perl (0.59-1) ... Setting up libmodule-implementation-perl (0.09-2) ... Setting up libpackage-stash-perl (0.40-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up liblist-someutils-perl (0.59-1) ... Setting up libmoox-aliases-perl (0.001006-2) ... Setting up libb-hooks-endofscope-perl (0.26-1) ... Setting up libnamespace-clean-perl (0.27-2) ... Setting up libwww-perl (6.72-1) ... Setting up libhtml-tokeparser-simple-perl (3.16-4) ... Setting up libwww-mechanize-perl (2.17-1) ... Setting up liblwp-protocol-https-perl (6.11-1) ... Processing triggers for libc-bin (2.37-13) ... Processing triggers for man-db (2.12.0-1) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for sgml-base (1.31) ... Setting up lintian (2.116.3) ... Setting up sbuild-build-depends-lintian-dummy:arm64 (0.invalid.0) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Running lintian... I: Lintian run was successful. +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 165008 Build-Time: 124 Distribution: unstable Foreign Architectures: arm64 Host Architecture: arm64 Install-Time: 57 Job: wise_2.4.1-23 Lintian: pass Machine Architecture: amd64 Package: wise Package-Time: 192 Source-Version: 2.4.1-23 Space: 165008 Status: successful Version: 2.4.1-23 -------------------------------------------------------------------------------- Finished at 2024-01-07T00:57:28Z Build needed 00:03:12, 165008k disk space