sbuild (Debian sbuild) 0.85.0 (04 January 2023) on debian-ci-siliconvalley +==============================================================================+ | wise 2.4.1-28 (s390x) Sun, 22 Feb 2026 17:15:09 +0000 | +==============================================================================+ Package: wise Version: 2.4.1-28 Source Version: 2.4.1-28 Distribution: unstable Machine Architecture: amd64 Host Architecture: s390x Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-19e3abce-58a6-4182-9f82-36ef7f2390f2' with '<>' I: NOTICE: Log filtering will replace 'build/wise-YAXRCj/resolver-ZanAOU' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://localhost:3142/debian unstable InRelease [187 kB] Get:2 http://localhost:3142/debian unstable/non-free Sources.diff/Index [63.3 kB] Get:3 http://localhost:3142/debian unstable/main Sources.diff/Index [63.6 kB] Get:4 http://localhost:3142/debian unstable/contrib Sources.diff/Index [63.3 kB] Get:5 http://localhost:3142/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:6 http://localhost:3142/debian unstable/non-free Sources T-2026-02-22-0202.11-F-2026-02-22-0202.11.pdiff [2236 B] Get:7 http://localhost:3142/debian unstable/main Sources T-2026-02-22-1403.43-F-2026-02-22-0202.11.pdiff [50.3 kB] Get:8 http://localhost:3142/debian unstable/contrib Sources T-2026-02-22-1403.43-F-2026-02-22-0802.29.pdiff [362 B] Get:6 http://localhost:3142/debian unstable/non-free Sources T-2026-02-22-0202.11-F-2026-02-22-0202.11.pdiff [2236 B] Get:9 http://localhost:3142/debian unstable/main amd64 Packages T-2026-02-22-1403.43-F-2026-02-22-0202.11.pdiff [55.7 kB] Get:8 http://localhost:3142/debian unstable/contrib Sources T-2026-02-22-1403.43-F-2026-02-22-0802.29.pdiff [362 B] Get:7 http://localhost:3142/debian unstable/main Sources T-2026-02-22-1403.43-F-2026-02-22-0202.11.pdiff [50.3 kB] Get:9 http://localhost:3142/debian unstable/main amd64 Packages T-2026-02-22-1403.43-F-2026-02-22-0202.11.pdiff [55.7 kB] Get:10 http://localhost:3142/debian unstable/main s390x Packages [9798 kB] Fetched 10.3 MB in 3s (3679 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 3454 kB of source archives. Get:1 http://localhost:3142/debian unstable/main wise 2.4.1-28 (dsc) [1820 B] Get:2 http://localhost:3142/debian unstable/main wise 2.4.1-28 (tar) [3410 kB] Get:3 http://localhost:3142/debian unstable/main wise 2.4.1-28 (diff) [42.2 kB] Fetched 3454 kB in 0s (152 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/wise-YAXRCj/wise-2.4.1' with '<>' I: NOTICE: Log filtering will replace 'build/wise-YAXRCj' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), texlive-latex-base, texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev, libfl-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-s390x:amd64, libc-dev:s390x, libstdc++-dev:s390x Filtered Build-Depends: debhelper-compat (= 13), texlive-latex-base, texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev, libfl-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-s390x:amd64, libc-dev:s390x, libstdc++-dev:s390x dpkg-deb: warning: root directory /<>/sbuild-build-depends-main-dummy has unusual owner or group 1000:119 dpkg-deb: hint: you might need to pass --root-owner-group, see for further details dpkg-deb: warning: ignoring 1 warning about the control file(s) 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 [805 B] Get:5 copy:/<>/apt_archive ./ Packages [848 B] Fetched 2262 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-s390x-linux-gnu bsdextrautils cpp-15-s390x-linux-gnu cpp-s390x-linux-gnu cross-exe-wrapper:s390x crossbuild-essential-s390x debhelper dh-autoreconf dh-strip-nondeterminism docbook docbook-to-man dwz fakeroot file flex fontconfig-config fonts-lmodern fonts-urw-base35 g++-15-s390x-linux-gnu g++-s390x-linux-gnu gcc-15-base:s390x gcc-15-cross-base gcc-15-s390x-linux-gnu gcc-15-s390x-linux-gnu-base gcc-s390x-linux-gnu gettext gettext-base ghostscript girepository-tools girepository-tools:s390x groff-base hevea hicolor-icon-theme imagemagick imagemagick-7-common imagemagick-7.q16 intltool-debian libarchive-zip-perl libasan8:s390x libasan8-s390x-cross libatomic1:s390x libatomic1-s390x-cross libavahi-client3 libavahi-common-data libavahi-common3 libblkid-dev:s390x libblkid1:s390x libbrotli1 libc-gconv-modules-extra:s390x libc6:s390x libc6-dev:s390x libc6-dev-s390x-cross libc6-s390x-cross libcairo2 libcom-err2 libcups2t64 libdatrie1 libdav1d7 libdbus-1-3 libde265-0 libdebhelper-perl libdeflate0 libelf1t64 libexpat1 libfakeroot libffi-dev:s390x libffi8 libffi8:s390x libfftw3-double3 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libfl-dev:s390x libfl2:s390x libfontconfig1 libfontenc1 libfreetype6 libgcc-15-dev:s390x libgcc-15-dev-s390x-cross libgcc-s1:s390x libgcc-s1-s390x-cross libgio-2.0-dev:s390x libgio-2.0-dev-bin libgirepository-2.0-0 libgirepository-2.0-0:s390x libglib2.0-0t64 libglib2.0-0t64:s390x libglib2.0-bin libglib2.0-data libglib2.0-dev:s390x libglib2.0-dev-bin libgnutls30t64 libgomp1:s390x libgomp1-s390x-cross libgraphite2-3 libgs-common libgs10 libgs10-common libgssapi-krb5-2 libharfbuzz0b libheif-plugin-dav1d libheif-plugin-libde265 libheif1 libice6 libicu76 libidn12 libidn2-0 libijs-0.35 libitm1:s390x libitm1-s390x-cross libjbig0 libjbig2dec0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkpathsea6 libkrb5-3 libkrb5support0 liblcms2-2 liblerc4 liblqr-1-0 liblsan0:s390x liblsan0-s390x-cross libltdl7 libmagic-mgc libmagic1t64 libmagickcore-7.q16-10 libmagickwand-7.q16-10 libmime-charset-perl libmount-dev:s390x libmount1:s390x libmpfi0 libncursesw6 libnetpbm11t64 libopenjp2-7 libosp5 libp11-kit0 libpaper-utils libpaper2 libpcre2-16-0:s390x libpcre2-32-0:s390x libpcre2-8-0:s390x libpcre2-dev:s390x libpcre2-posix3:s390x libpipeline1 libpixman-1-0 libpkgconf7 libpng16-16t64 libpotrace0 libproc2-0 libptexenc1 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libraw23t64 libreadline8t64 libselinux-dev:s390x libselinux1:s390x libsepol-dev:s390x libsepol2:s390x libsharpyuv0 libsm6 libsombok3 libsqlite3-0 libstdc++-15-dev:s390x libstdc++-15-dev-s390x-cross libstdc++6:s390x libstdc++6-s390x-cross libsynctex2 libsysprof-capture-4-dev:s390x libtasn1-6 libteckit0 libtexlua53-5 libtext-charwidth-perl libtext-wrapi18n-perl libthai-data libthai0 libtiff6 libtool libtsan2:s390x libtsan2-s390x-cross libubsan1:s390x libubsan1-s390x-cross libuchardet0 libunicode-linebreak-perl libunistring5 libuuid1:s390x libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2-16 libxmu6 libxpm4 libxrender1 libxt6t64 libyaml-tiny-perl libzzip-0-13t64 linux-libc-dev-s390x-cross lmodern m4 man-db media-types native-architecture netbase netpbm opensp pkgconf:s390x pkgconf-bin po-debconf poppler-data procps python3 python3-minimal python3-packaging python3.13 python3.13-minimal qemu-user 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:s390x x11-common xdg-utils xfonts-encodings xfonts-utils xml-core zlib1g:s390x zlib1g-dev:s390x Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-15-locales cpp-15-doc cpp-doc dh-make docbook-defguide docbook-dsssl docbook-xml psgml bison flex-doc fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre gcc-15-doc manpages-dev gdb-s390x-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff hevea-doc texlive-latex-extra imagemagick-7-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:s390x libc-l10n:s390x locales:s390x libnss-nis:s390x libnss-nisplus:s390x manpages-dev:s390x cups-common libfftw3-bin libfftw3-dev gir1.2-glib-2.0-dev:s390x libglib2.0-doc:s390x libgdk-pixbuf2.0-bin libxml2-utils low-memory-monitor low-memory-monitor:s390x gnutls-bin krb5-doc krb5-user libheif-plugin-ffmpegdec libheif-plugin-jpegdec libheif-plugin-jpegenc libheif-plugin-j2kdec libheif-plugin-j2kenc libheif-plugin-kvazaar libheif-plugin-rav1e libheif-plugin-svtenc liblcms2-utils libmagickcore-7.q16-10-extra libencode-eucjpascii-perl libencode-hanextra-perl libpod2-base-perl cryptsetup-bin:s390x libmpfi-doc libstdc++-15-doc:s390x libtool-doc gfortran | fortran95-compiler uuid-runtime:s390x 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 python3.13-venv python3.13-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: libfl-dev curl | wget | lynx libmagickcore-7.q16-10-extra libidn2-0:s390x dbus libarchive-cpio-perl shared-mime-info xdg-user-dirs shared-mime-info:s390x xdg-user-dirs:s390x fonts-droid-fallback libheif-plugin-x265 libheif-plugin-aomenc krb5-locales libgpm2 libltdl-dev libmail-sendmail-perl psmisc linux-sysctl-defaults ca-certificates qemu-user-binfmt 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-s390x-linux-gnu bsdextrautils cpp-15-s390x-linux-gnu cpp-s390x-linux-gnu cross-exe-wrapper:s390x crossbuild-essential-s390x debhelper dh-autoreconf dh-strip-nondeterminism docbook docbook-to-man dwz fakeroot file flex fontconfig-config fonts-lmodern fonts-urw-base35 g++-15-s390x-linux-gnu g++-s390x-linux-gnu gcc-15-base:s390x gcc-15-cross-base gcc-15-s390x-linux-gnu gcc-15-s390x-linux-gnu-base gcc-s390x-linux-gnu gettext gettext-base ghostscript girepository-tools girepository-tools:s390x groff-base hevea hicolor-icon-theme imagemagick imagemagick-7-common imagemagick-7.q16 intltool-debian libarchive-zip-perl libasan8:s390x libasan8-s390x-cross libatomic1:s390x libatomic1-s390x-cross libavahi-client3 libavahi-common-data libavahi-common3 libblkid-dev:s390x libblkid1:s390x libbrotli1 libc-gconv-modules-extra:s390x libc6:s390x libc6-dev:s390x libc6-dev-s390x-cross libc6-s390x-cross libcairo2 libcom-err2 libcups2t64 libdatrie1 libdav1d7 libdbus-1-3 libde265-0 libdebhelper-perl libdeflate0 libelf1t64 libexpat1 libfakeroot libffi-dev:s390x libffi8 libffi8:s390x libfftw3-double3 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libfl-dev:s390x libfl2:s390x libfontconfig1 libfontenc1 libfreetype6 libgcc-15-dev:s390x libgcc-15-dev-s390x-cross libgcc-s1:s390x libgcc-s1-s390x-cross libgio-2.0-dev:s390x libgio-2.0-dev-bin libgirepository-2.0-0 libgirepository-2.0-0:s390x libglib2.0-0t64 libglib2.0-0t64:s390x libglib2.0-bin libglib2.0-data libglib2.0-dev:s390x libglib2.0-dev-bin libgnutls30t64 libgomp1:s390x libgomp1-s390x-cross libgraphite2-3 libgs-common libgs10 libgs10-common libgssapi-krb5-2 libharfbuzz0b libheif-plugin-dav1d libheif-plugin-libde265 libheif1 libice6 libicu76 libidn12 libidn2-0 libijs-0.35 libitm1:s390x libitm1-s390x-cross libjbig0 libjbig2dec0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkpathsea6 libkrb5-3 libkrb5support0 liblcms2-2 liblerc4 liblqr-1-0 liblsan0:s390x liblsan0-s390x-cross libltdl7 libmagic-mgc libmagic1t64 libmagickcore-7.q16-10 libmagickwand-7.q16-10 libmime-charset-perl libmount-dev:s390x libmount1:s390x libmpfi0 libncursesw6 libnetpbm11t64 libopenjp2-7 libosp5 libp11-kit0 libpaper-utils libpaper2 libpcre2-16-0:s390x libpcre2-32-0:s390x libpcre2-8-0:s390x libpcre2-dev:s390x libpcre2-posix3:s390x libpipeline1 libpixman-1-0 libpkgconf7 libpng16-16t64 libpotrace0 libproc2-0 libptexenc1 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libraw23t64 libreadline8t64 libselinux-dev:s390x libselinux1:s390x libsepol-dev:s390x libsepol2:s390x libsharpyuv0 libsm6 libsombok3 libsqlite3-0 libstdc++-15-dev:s390x libstdc++-15-dev-s390x-cross libstdc++6:s390x libstdc++6-s390x-cross libsynctex2 libsysprof-capture-4-dev:s390x libtasn1-6 libteckit0 libtexlua53-5 libtext-charwidth-perl libtext-wrapi18n-perl libthai-data libthai0 libtiff6 libtool libtsan2:s390x libtsan2-s390x-cross libubsan1:s390x libubsan1-s390x-cross libuchardet0 libunicode-linebreak-perl libunistring5 libuuid1:s390x libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6 libxml2-16 libxmu6 libxpm4 libxrender1 libxt6t64 libyaml-tiny-perl libzzip-0-13t64 linux-libc-dev-s390x-cross lmodern m4 man-db media-types native-architecture netbase netpbm opensp pkgconf:s390x pkgconf-bin po-debconf poppler-data procps python3 python3-minimal python3-packaging python3.13 python3.13-minimal qemu-user readline-common sbuild-build-depends-main-dummy:s390x 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:s390x x11-common xdg-utils xfonts-encodings xfonts-utils xml-core zlib1g:s390x zlib1g-dev:s390x 0 upgraded, 253 newly installed, 0 to remove and 0 not upgraded. Need to get 411 MB of archives. After this operation, 1435 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 unstable/main amd64 m4 amd64 1.4.21-1 [332 kB] Get:3 http://localhost:3142/debian unstable/main amd64 flex amd64 2.6.4-8.2+b5 [425 kB] Get:4 http://localhost:3142/debian unstable/main amd64 libexpat1 amd64 2.7.4-1 [116 kB] Get:5 http://localhost:3142/debian unstable/main amd64 libfftw3-double3 amd64 3.3.10-2+b2 [775 kB] Get:6 http://localhost:3142/debian unstable/main amd64 libbrotli1 amd64 1.2.0-3 [320 kB] Get:7 http://localhost:3142/debian unstable/main amd64 libpng16-16t64 amd64 1.6.55-1 [288 kB] Get:8 http://localhost:3142/debian unstable/main amd64 libfreetype6 amd64 2.14.1+dfsg-2 [493 kB] Get:9 http://localhost:3142/debian unstable/main amd64 libfontenc1 amd64 1:1.1.8-1+b3 [23.4 kB] Get:10 http://localhost:3142/debian unstable/main amd64 x11-common all 1:7.7+26 [217 kB] Get:11 http://localhost:3142/debian unstable/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get:12 http://localhost:3142/debian unstable/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get:13 http://localhost:3142/debian unstable/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get:14 http://localhost:3142/debian unstable/main amd64 fontconfig-config amd64 2.17.1-5 [56.1 kB] Get:15 http://localhost:3142/debian unstable/main amd64 libfontconfig1 amd64 2.17.1-5 [132 kB] Get:16 http://localhost:3142/debian unstable/main amd64 libsharpyuv0 amd64 1.5.0-0.1+b1 [116 kB] Get:17 http://localhost:3142/debian unstable/main amd64 libde265-0 amd64 1.0.16-1+b1 [195 kB] Get:18 http://localhost:3142/debian unstable/main amd64 libheif-plugin-libde265 amd64 1.21.2-3 [18.0 kB] Get:19 http://localhost:3142/debian unstable/main amd64 libdav1d7 amd64 1.5.3-1+b1 [564 kB] Get:20 http://localhost:3142/debian unstable/main amd64 libheif-plugin-dav1d amd64 1.21.2-3 [20.6 kB] Get:21 http://localhost:3142/debian unstable/main amd64 libheif1 amd64 1.21.2-3 [650 kB] Get:22 http://localhost:3142/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b3 [32.2 kB] Get:23 http://localhost:3142/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-4 [168 kB] Get:24 http://localhost:3142/debian unstable/main amd64 liblcms2-2 amd64 2.17-1 [163 kB] Get:25 http://localhost:3142/debian unstable/main amd64 libffi8 amd64 3.5.2-3+b1 [26.4 kB] Get:26 http://localhost:3142/debian unstable/main amd64 libglib2.0-0t64 amd64 2.87.2-3 [1552 kB] Get:27 http://localhost:3142/debian unstable/main amd64 liblqr-1-0 amd64 0.4.2-2.2 [29.7 kB] Get:28 http://localhost:3142/debian unstable/main amd64 libltdl7 amd64 2.5.4-9 [416 kB] Get:29 http://localhost:3142/debian unstable/main amd64 libopenjp2-7 amd64 2.5.4-1 [206 kB] Get:30 http://localhost:3142/debian unstable/main amd64 libraw23t64 amd64 0.21.5b-1 [393 kB] Get:31 http://localhost:3142/debian unstable/main amd64 libdeflate0 amd64 1.23-2+b1 [49.5 kB] Get:32 http://localhost:3142/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5+b1 [199 kB] Get:33 http://localhost:3142/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1+b1 [336 kB] Get:34 http://localhost:3142/debian unstable/main amd64 libtiff6 amd64 4.7.1-1 [361 kB] Get:35 http://localhost:3142/debian unstable/main amd64 libwebpdemux2 amd64 1.5.0-0.1+b1 [114 kB] Get:36 http://localhost:3142/debian unstable/main amd64 libwebpmux3 amd64 1.5.0-0.1+b1 [126 kB] Get:37 http://localhost:3142/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1+b1 [20.8 kB] Get:38 http://localhost:3142/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-2 [27.9 kB] Get:39 http://localhost:3142/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b2 [144 kB] Get:40 http://localhost:3142/debian unstable/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get:41 http://localhost:3142/debian unstable/main amd64 libx11-6 amd64 2:1.8.12-1+b1 [824 kB] Get:42 http://localhost:3142/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b4 [50.7 kB] Get:43 http://localhost:3142/debian unstable/main amd64 libxml2-16 amd64 2.15.1+dfsg-2+b1 [641 kB] Get:44 http://localhost:3142/debian unstable/main amd64 imagemagick-7-common all 8:7.1.2.13+dfsg1-1 [70.2 kB] Get:45 http://localhost:3142/debian unstable/main amd64 libmagickcore-7.q16-10 amd64 8:7.1.2.13+dfsg1-1 [1852 kB] Get:46 http://localhost:3142/debian unstable/main amd64 libmagickwand-7.q16-10 amd64 8:7.1.2.13+dfsg1-1 [343 kB] Get:47 http://localhost:3142/debian unstable/main amd64 poppler-data all 0.4.12-1 [1601 kB] Get:48 http://localhost:3142/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.12-1 [866 kB] Get:49 http://localhost:3142/debian unstable/main amd64 python3.13-minimal amd64 3.13.12-1 [2267 kB] Get:50 http://localhost:3142/debian unstable/main amd64 python3-minimal amd64 3.13.9-3 [27.6 kB] Get:51 http://localhost:3142/debian unstable/main amd64 media-types all 14.0.0 [30.8 kB] Get:52 http://localhost:3142/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get:53 http://localhost:3142/debian unstable/main amd64 libncursesw6 amd64 6.6+20251231-1 [137 kB] Get:54 http://localhost:3142/debian unstable/main amd64 readline-common all 8.3-4 [74.8 kB] Get:55 http://localhost:3142/debian unstable/main amd64 libreadline8t64 amd64 8.3-4 [181 kB] Get:56 http://localhost:3142/debian unstable/main amd64 libsqlite3-0 amd64 3.46.1-9 [920 kB] Get:57 http://localhost:3142/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.12-1 [1974 kB] Get:58 http://localhost:3142/debian unstable/main amd64 python3.13 amd64 3.13.12-1 [776 kB] Get:59 http://localhost:3142/debian unstable/main amd64 libpython3-stdlib amd64 3.13.9-3 [10.5 kB] Get:60 http://localhost:3142/debian unstable/main amd64 python3 amd64 3.13.9-3 [27.6 kB] Get:61 http://localhost:3142/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-9+b1 [66.1 kB] Get:62 http://localhost:3142/debian unstable/main amd64 procps amd64 2:4.0.4-9+b1 [883 kB] Get:63 http://localhost:3142/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get:64 http://localhost:3142/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5+b1 [338 kB] Get:65 http://localhost:3142/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5+b1 [110 kB] Get:66 http://localhost:3142/debian unstable/main amd64 file amd64 1:5.46-5+b1 [43.8 kB] Get:67 http://localhost:3142/debian unstable/main amd64 gettext-base amd64 0.23.2-1 [245 kB] Get:68 http://localhost:3142/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2+b1 [68.8 kB] Get:69 http://localhost:3142/debian unstable/main amd64 groff-base amd64 1.23.0-10 [1194 kB] Get:70 http://localhost:3142/debian unstable/main amd64 bsdextrautils amd64 2.41.3-4 [98.9 kB] Get:71 http://localhost:3142/debian unstable/main amd64 libpipeline1 amd64 1.5.8-2 [42.1 kB] Get:72 http://localhost:3142/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:73 http://localhost:3142/debian unstable/main amd64 libtext-charwidth-perl amd64 0.04-11+b5 [9532 B] Get:74 http://localhost:3142/debian unstable/main amd64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get:75 http://localhost:3142/debian unstable/main amd64 ucf all 3.0052 [43.3 kB] Get:76 http://localhost:3142/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get:77 http://localhost:3142/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get:78 http://localhost:3142/debian unstable/main amd64 automake all 1:1.18.1-3 [878 kB] Get:79 http://localhost:3142/debian unstable/main amd64 autopoint all 0.23.2-1 [772 kB] Get:80 http://localhost:3142/debian unstable/main amd64 binutils-s390x-linux-gnu amd64 2.46-2 [1369 kB] Get:81 http://localhost:3142/debian unstable/main amd64 gcc-15-s390x-linux-gnu-base amd64 15.2.0-13cross1 [55.1 kB] Get:82 http://localhost:3142/debian unstable/main amd64 cpp-15-s390x-linux-gnu amd64 15.2.0-13cross1 [10.2 MB] Get:83 http://localhost:3142/debian unstable/main amd64 cpp-s390x-linux-gnu amd64 4:15.2.0-5 [5328 B] Get:84 http://localhost:3142/debian unstable/main s390x gcc-15-base s390x 15.2.0-13 [54.8 kB] Get:85 http://localhost:3142/debian unstable/main s390x libgcc-s1 s390x 15.2.0-13 [31.8 kB] Get:86 http://localhost:3142/debian unstable/main s390x libc-gconv-modules-extra s390x 2.42-13 [1101 kB] Get:87 http://localhost:3142/debian unstable/main s390x libc6 s390x 2.42-13 [1433 kB] Get:88 http://localhost:3142/debian unstable/main amd64 qemu-user amd64 1:10.2.1+ds-1 [70.4 MB] Get:89 http://localhost:3142/debian unstable/main s390x cross-exe-wrapper s390x 0.2.6+b1 [6900 B] Get:90 http://localhost:3142/debian unstable/main amd64 gcc-15-cross-base all 15.2.0-13cross1 [50.4 kB] Get:91 http://localhost:3142/debian unstable/main amd64 libc6-s390x-cross all 2.42-12cross1 [1182 kB] Get:92 http://localhost:3142/debian unstable/main amd64 libgcc-s1-s390x-cross all 15.2.0-13cross1 [31.8 kB] Get:93 http://localhost:3142/debian unstable/main amd64 libgomp1-s390x-cross all 15.2.0-13cross1 [132 kB] Get:94 http://localhost:3142/debian unstable/main amd64 libitm1-s390x-cross all 15.2.0-13cross1 [26.4 kB] Get:95 http://localhost:3142/debian unstable/main amd64 libatomic1-s390x-cross all 15.2.0-13cross1 [8448 B] Get:96 http://localhost:3142/debian unstable/main amd64 libasan8-s390x-cross all 15.2.0-13cross1 [2592 kB] Get:97 http://localhost:3142/debian unstable/main amd64 liblsan0-s390x-cross all 15.2.0-13cross1 [1215 kB] Get:98 http://localhost:3142/debian unstable/main amd64 libtsan2-s390x-cross all 15.2.0-13cross1 [2349 kB] Get:99 http://localhost:3142/debian unstable/main amd64 libstdc++6-s390x-cross all 15.2.0-13cross1 [731 kB] Get:100 http://localhost:3142/debian unstable/main amd64 libubsan1-s390x-cross all 15.2.0-13cross1 [1082 kB] Get:101 http://localhost:3142/debian unstable/main amd64 libgcc-15-dev-s390x-cross all 15.2.0-13cross1 [1098 kB] Get:102 http://localhost:3142/debian unstable/main amd64 gcc-15-s390x-linux-gnu amd64 15.2.0-13cross1 [19.2 MB] Get:103 http://localhost:3142/debian unstable/main amd64 gcc-s390x-linux-gnu amd64 4:15.2.0-5 [1440 B] Get:104 http://localhost:3142/debian unstable/main amd64 linux-libc-dev-s390x-cross all 6.18.12-1 [12.2 kB] Get:105 http://localhost:3142/debian unstable/main amd64 libc6-dev-s390x-cross all 2.42-12cross1 [1572 kB] Get:106 http://localhost:3142/debian unstable/main amd64 libstdc++-15-dev-s390x-cross all 15.2.0-13cross1 [2444 kB] Get:107 http://localhost:3142/debian unstable/main amd64 g++-15-s390x-linux-gnu amd64 15.2.0-13cross1 [11.2 MB] Get:108 http://localhost:3142/debian unstable/main amd64 g++-s390x-linux-gnu amd64 4:15.2.0-5 [1200 B] Get:109 http://localhost:3142/debian unstable/main amd64 crossbuild-essential-s390x all 12.12 [3548 B] Get:110 http://localhost:3142/debian unstable/main amd64 libdebhelper-perl all 13.30 [92.7 kB] Get:111 http://localhost:3142/debian unstable/main amd64 libtool all 2.5.4-9 [540 kB] Get:112 http://localhost:3142/debian unstable/main amd64 dh-autoreconf all 21+nmu1 [11.7 kB] Get:113 http://localhost:3142/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:114 http://localhost:3142/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get:115 http://localhost:3142/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get:116 http://localhost:3142/debian unstable/main amd64 libelf1t64 amd64 0.194-1 [185 kB] Get:117 http://localhost:3142/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get:118 http://localhost:3142/debian unstable/main amd64 libunistring5 amd64 1.3-2+b1 [466 kB] Get:119 http://localhost:3142/debian unstable/main amd64 gettext amd64 0.23.2-1 [1687 kB] Get:120 http://localhost:3142/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:121 http://localhost:3142/debian unstable/main amd64 po-debconf all 1.0.22 [216 kB] Get:122 http://localhost:3142/debian unstable/main amd64 debhelper all 13.30 [942 kB] Get:123 http://localhost:3142/debian unstable/main amd64 sgml-base all 1.31+nmu1 [10.9 kB] Get:124 http://localhost:3142/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get:125 http://localhost:3142/debian unstable/main amd64 sgml-data all 2.0.11+nmu1 [179 kB] Get:126 http://localhost:3142/debian unstable/main amd64 docbook all 4.5-11 [126 kB] Get:127 http://localhost:3142/debian unstable/main amd64 libosp5 amd64 1.5.2-15.2 [972 kB] Get:128 http://localhost:3142/debian unstable/main amd64 opensp amd64 1.5.2-15.2 [448 kB] Get:129 http://localhost:3142/debian unstable/main amd64 docbook-to-man amd64 1:2.0.0-50 [74.5 kB] Get:130 http://localhost:3142/debian unstable/main amd64 libfakeroot amd64 1.37.2-1 [29.9 kB] Get:131 http://localhost:3142/debian unstable/main amd64 fakeroot amd64 1.37.2-1 [76.2 kB] Get:132 http://localhost:3142/debian unstable/main amd64 fonts-lmodern all 2.005-1 [4540 kB] Get:133 http://localhost:3142/debian unstable/main amd64 libgs-common all 10.06.0~dfsg-3 [149 kB] Get:134 http://localhost:3142/debian unstable/main amd64 libgs10-common all 10.06.0~dfsg-3 [479 kB] Get:135 http://localhost:3142/debian unstable/main amd64 libavahi-common-data amd64 0.8-18 [113 kB] Get:136 http://localhost:3142/debian unstable/main amd64 libavahi-common3 amd64 0.8-18 [45.2 kB] Get:137 http://localhost:3142/debian unstable/main amd64 libdbus-1-3 amd64 1.16.2-3 [179 kB] Get:138 http://localhost:3142/debian unstable/main amd64 libavahi-client3 amd64 0.8-18 [49.2 kB] Get:139 http://localhost:3142/debian unstable/main amd64 libidn2-0 amd64 2.3.8-4+b1 [110 kB] Get:140 http://localhost:3142/debian unstable/main amd64 libp11-kit0 amd64 0.26.2-2 [470 kB] Get:141 http://localhost:3142/debian unstable/main amd64 libtasn1-6 amd64 4.21.0-2 [50.4 kB] Get:142 http://localhost:3142/debian unstable/main amd64 libgnutls30t64 amd64 3.8.12-3 [1520 kB] Get:143 http://localhost:3142/debian unstable/main amd64 libkrb5support0 amd64 1.22.1-2 [33.1 kB] Get:144 http://localhost:3142/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b8 [25.1 kB] Get:145 http://localhost:3142/debian unstable/main amd64 libk5crypto3 amd64 1.22.1-2 [81.1 kB] Get:146 http://localhost:3142/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6+b1 [9784 B] Get:147 http://localhost:3142/debian unstable/main amd64 libkrb5-3 amd64 1.22.1-2 [337 kB] Get:148 http://localhost:3142/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.22.1-2 [139 kB] Get:149 http://localhost:3142/debian unstable/main amd64 libcups2t64 amd64 2.4.16-1 [254 kB] Get:150 http://localhost:3142/debian unstable/main amd64 libidn12 amd64 1.43-2+b1 [49.0 kB] Get:151 http://localhost:3142/debian unstable/main amd64 libijs-0.35 amd64 0.35-16+b1 [15.3 kB] Get:152 http://localhost:3142/debian unstable/main amd64 libjbig2dec0 amd64 0.20-1+b4 [65.3 kB] Get:153 http://localhost:3142/debian unstable/main amd64 libpaper2 amd64 2.2.5-0.3+b3 [16.7 kB] Get:154 http://localhost:3142/debian unstable/main amd64 libice6 amd64 2:1.1.1-1+b1 [66.8 kB] Get:155 http://localhost:3142/debian unstable/main amd64 libsm6 amd64 2:1.2.6-1+b1 [37.9 kB] Get:156 http://localhost:3142/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.3+b1 [191 kB] Get:157 http://localhost:3142/debian unstable/main amd64 libgs10 amd64 10.06.0~dfsg-3 [2909 kB] Get:158 http://localhost:3142/debian unstable/main amd64 ghostscript amd64 10.06.0~dfsg-3 [50.6 kB] Get:159 http://localhost:3142/debian unstable/main amd64 native-architecture all 0.2.6 [2264 B] Get:160 http://localhost:3142/debian unstable/main amd64 libgirepository-2.0-0 amd64 2.87.2-3 [147 kB] Get:161 http://localhost:3142/debian unstable/main amd64 girepository-tools amd64 2.87.2-3 [153 kB] Get:162 http://localhost:3142/debian unstable/main s390x libffi8 s390x 3.5.2-3+b1 [23.3 kB] Get:163 http://localhost:3142/debian unstable/main s390x libatomic1 s390x 15.2.0-13 [8728 B] Get:164 http://localhost:3142/debian unstable/main s390x libblkid1 s390x 2.41.3-4 [168 kB] Get:165 http://localhost:3142/debian unstable/main s390x libpcre2-8-0 s390x 10.46-1+b1 [298 kB] Get:166 http://localhost:3142/debian unstable/main s390x libselinux1 s390x 3.9-4+b1 [83.6 kB] Get:167 http://localhost:3142/debian unstable/main s390x libmount1 s390x 2.41.3-4 [202 kB] Get:168 http://localhost:3142/debian unstable/main s390x zlib1g s390x 1:1.3.dfsg+really1.3.1-3 [86.6 kB] Get:169 http://localhost:3142/debian unstable/main s390x libglib2.0-0t64 s390x 2.87.2-3 [1459 kB] Get:170 http://localhost:3142/debian unstable/main s390x libgirepository-2.0-0 s390x 2.87.2-3 [146 kB] Get:171 http://localhost:3142/debian unstable/main s390x girepository-tools s390x 2.87.2-3 [150 kB] Get:172 http://localhost:3142/debian unstable/main amd64 libnetpbm11t64 amd64 2:11.13.03-1 [187 kB] Get:173 http://localhost:3142/debian unstable/main amd64 netpbm amd64 2:11.13.03-1 [2093 kB] Get:174 http://localhost:3142/debian unstable/main amd64 tex-common all 6.20 [29.7 kB] Get:175 http://localhost:3142/debian unstable/main amd64 libpaper-utils amd64 2.2.5-0.3+b3 [16.5 kB] Get:176 http://localhost:3142/debian unstable/main amd64 libkpathsea6 amd64 2025.20250727.75242+ds-5 [159 kB] Get:177 http://localhost:3142/debian unstable/main amd64 libptexenc1 amd64 2025.20250727.75242+ds-5 [54.3 kB] Get:178 http://localhost:3142/debian unstable/main amd64 libsynctex2 amd64 2025.20250727.75242+ds-5 [65.0 kB] Get:179 http://localhost:3142/debian unstable/main amd64 libtexlua53-5 amd64 2025.20250727.75242+ds-5 [116 kB] Get:180 http://localhost:3142/debian unstable/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get:181 http://localhost:3142/debian unstable/main amd64 libpixman-1-0 amd64 0.46.4-1+b1 [259 kB] Get:182 http://localhost:3142/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b2 [115 kB] Get:183 http://localhost:3142/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b2 [105 kB] Get:184 http://localhost:3142/debian unstable/main amd64 libxrender1 amd64 1:0.9.12-1+b1 [27.7 kB] Get:185 http://localhost:3142/debian unstable/main amd64 libcairo2 amd64 1.18.4-3 [544 kB] Get:186 http://localhost:3142/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-11+b1 [77.0 kB] Get:187 http://localhost:3142/debian unstable/main amd64 libharfbuzz0b amd64 12.3.2-2 [514 kB] Get:188 http://localhost:3142/debian unstable/main amd64 libicu76 amd64 76.1-4+b1 [9752 kB] Get:189 http://localhost:3142/debian unstable/main amd64 libmpfi0 amd64 1.5.4+ds-4+b1 [36.7 kB] Get:190 http://localhost:3142/debian unstable/main amd64 libpotrace0 amd64 1.16-2+b3 [25.5 kB] Get:191 http://localhost:3142/debian unstable/main amd64 libteckit0 amd64 2.5.13+ds-1 [369 kB] Get:192 http://localhost:3142/debian unstable/main amd64 libxmu6 amd64 2:1.1.3-4 [59.4 kB] Get:193 http://localhost:3142/debian unstable/main amd64 libxpm4 amd64 1:3.5.17-1+b4 [56.6 kB] Get:194 http://localhost:3142/debian unstable/main amd64 libxaw7 amd64 2:1.0.16-1+b1 [215 kB] Get:195 http://localhost:3142/debian unstable/main amd64 libxi6 amd64 2:1.8.2-2 [79.8 kB] Get:196 http://localhost:3142/debian unstable/main amd64 libzzip-0-13t64 amd64 0.13.78+dfsg.1-0.2 [59.2 kB] Get:197 http://localhost:3142/debian unstable/main amd64 texlive-binaries amd64 2025.20250727.75242+ds-5 [8692 kB] Get:198 http://localhost:3142/debian unstable/main amd64 xdg-utils all 1.2.1-2 [75.8 kB] Get:199 http://localhost:3142/debian unstable/main amd64 texlive-base all 2025.20260124-1 [23.1 MB] Get:200 http://localhost:3142/debian unstable/main amd64 hicolor-icon-theme all 0.18-2 [11.8 kB] Get:201 http://localhost:3142/debian unstable/main amd64 imagemagick-7.q16 amd64 8:7.1.2.13+dfsg1-1 [729 kB] Get:202 http://localhost:3142/debian unstable/main amd64 imagemagick amd64 8:7.1.2.13+dfsg1-1 [22.7 kB] Get:203 http://localhost:3142/debian unstable/main amd64 hevea amd64 2.36-2+b5 [2102 kB] Get:204 http://localhost:3142/debian unstable/main s390x libasan8 s390x 15.2.0-13 [2599 kB] Get:205 http://localhost:3142/debian unstable/main s390x libc6-dev s390x 2.42-13 [1578 kB] Get:206 http://localhost:3142/debian unstable/main s390x libuuid1 s390x 2.41.3-4 [39.2 kB] Get:207 http://localhost:3142/debian unstable/main s390x uuid-dev s390x 2.41.3-4 [50.3 kB] Get:208 http://localhost:3142/debian unstable/main s390x libblkid-dev s390x 2.41.3-4 [206 kB] Get:209 http://localhost:3142/debian unstable/main amd64 libdatrie1 amd64 0.2.14-1 [39.6 kB] Get:210 http://localhost:3142/debian unstable/main s390x libffi-dev s390x 3.5.2-3+b1 [59.5 kB] Get:211 http://localhost:3142/debian unstable/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get:212 http://localhost:3142/debian unstable/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get:213 http://localhost:3142/debian unstable/main s390x libfl2 s390x 2.6.4-8.2+b5 [84.2 kB] Get:214 http://localhost:3142/debian unstable/main s390x libfl-dev s390x 2.6.4-8.2+b5 [85.5 kB] Get:215 http://localhost:3142/debian unstable/main s390x libgomp1 s390x 15.2.0-13 [134 kB] Get:216 http://localhost:3142/debian unstable/main s390x libitm1 s390x 15.2.0-13 [26.9 kB] Get:217 http://localhost:3142/debian unstable/main s390x liblsan0 s390x 15.2.0-13 [1217 kB] Get:218 http://localhost:3142/debian unstable/main s390x libtsan2 s390x 15.2.0-13 [2357 kB] Get:219 http://localhost:3142/debian unstable/main s390x libstdc++6 s390x 15.2.0-13 [782 kB] Get:220 http://localhost:3142/debian unstable/main s390x libubsan1 s390x 15.2.0-13 [1083 kB] Get:221 http://localhost:3142/debian unstable/main s390x libgcc-15-dev s390x 15.2.0-13 [1103 kB] Get:222 http://localhost:3142/debian unstable/main s390x libsepol2 s390x 3.9-2 [281 kB] Get:223 http://localhost:3142/debian unstable/main s390x libsepol-dev s390x 3.9-2 [361 kB] Get:224 http://localhost:3142/debian unstable/main s390x libpcre2-16-0 s390x 10.46-1+b1 [282 kB] Get:225 http://localhost:3142/debian unstable/main s390x libpcre2-32-0 s390x 10.46-1+b1 [270 kB] Get:226 http://localhost:3142/debian unstable/main s390x libpcre2-posix3 s390x 10.46-1+b1 [64.1 kB] Get:227 http://localhost:3142/debian unstable/main s390x libpcre2-dev s390x 10.46-1+b1 [868 kB] Get:228 http://localhost:3142/debian unstable/main s390x libselinux-dev s390x 3.9-4+b1 [168 kB] Get:229 http://localhost:3142/debian unstable/main s390x libmount-dev s390x 2.41.3-4 [32.1 kB] Get:230 http://localhost:3142/debian unstable/main s390x libsysprof-capture-4-dev s390x 50~beta-1 [47.3 kB] Get:231 http://localhost:3142/debian unstable/main amd64 libpkgconf7 amd64 2.5.1-4 [47.8 kB] Get:232 http://localhost:3142/debian unstable/main amd64 pkgconf-bin amd64 2.5.1-4 [35.9 kB] Get:233 http://localhost:3142/debian unstable/main s390x pkgconf s390x 2.5.1-4 [33.6 kB] Get:234 http://localhost:3142/debian unstable/main s390x zlib1g-dev s390x 1:1.3.dfsg+really1.3.1-3 [917 kB] Get:235 http://localhost:3142/debian unstable/main s390x libgio-2.0-dev s390x 2.87.2-3 [1655 kB] Get:236 http://localhost:3142/debian unstable/main amd64 python3-packaging all 25.0-2 [56.7 kB] Get:237 http://localhost:3142/debian unstable/main amd64 libgio-2.0-dev-bin amd64 2.87.2-3 [171 kB] Get:238 http://localhost:3142/debian unstable/main amd64 libglib2.0-data all 2.87.2-3 [1292 kB] Get:239 http://localhost:3142/debian unstable/main amd64 libglib2.0-bin amd64 2.87.2-3 [134 kB] Get:240 http://localhost:3142/debian unstable/main amd64 libglib2.0-dev-bin amd64 2.87.2-3 [58.1 kB] Get:241 http://localhost:3142/debian unstable/main s390x libglib2.0-dev s390x 2.87.2-3 [58.8 kB] Get:242 http://localhost:3142/debian unstable/main amd64 libmime-charset-perl all 1.013.1-2 [34.0 kB] Get:243 http://localhost:3142/debian unstable/main amd64 libthai-data all 0.1.30-1 [172 kB] Get:244 http://localhost:3142/debian unstable/main amd64 libthai0 amd64 0.1.30-1 [52.2 kB] Get:245 http://localhost:3142/debian unstable/main amd64 libsombok3 amd64 2.4.0-2+b3 [32.2 kB] Get:246 http://localhost:3142/debian unstable/main s390x libstdc++-15-dev s390x 15.2.0-13 [2466 kB] Get:247 http://localhost:3142/debian unstable/main amd64 libunicode-linebreak-perl amd64 0.0.20190101-3 [95.7 kB] Get:248 http://localhost:3142/debian unstable/main amd64 libyaml-tiny-perl all 1.76-1 [29.8 kB] Get:249 http://localhost:3142/debian unstable/main amd64 lmodern all 2.005-1 [9480 kB] Get:250 http://localhost:3142/debian unstable/main amd64 texlive-latex-base all 2025.20260124-1 [1340 kB] Get:251 http://localhost:3142/debian unstable/main amd64 texlive-luatex all 2025.20260124-1 [36.9 MB] Get:252 http://localhost:3142/debian unstable/main amd64 texlive-plain-generic all 2025.20260124-1 [29.9 MB] Get:253 http://localhost:3142/debian unstable/main amd64 texlive-extra-utils all 2025.20260124-1 [70.7 MB] Preconfiguring packages ... Fetched 411 MB in 2s (201 MB/s) Selecting previously unselected package m4. (Reading database ... 12980 files and directories currently installed.) Preparing to unpack .../00-m4_1.4.21-1_amd64.deb ... Unpacking m4 (1.4.21-1) ... Selecting previously unselected package flex. Preparing to unpack .../01-flex_2.6.4-8.2+b5_amd64.deb ... Unpacking flex (2.6.4-8.2+b5) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../02-libexpat1_2.7.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.4-1) ... Selecting previously unselected package libfftw3-double3:amd64. Preparing to unpack .../03-libfftw3-double3_3.3.10-2+b2_amd64.deb ... Unpacking libfftw3-double3:amd64 (3.3.10-2+b2) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../04-libbrotli1_1.2.0-3_amd64.deb ... Unpacking libbrotli1:amd64 (1.2.0-3) ... Selecting previously unselected package libpng16-16t64:amd64. Preparing to unpack .../05-libpng16-16t64_1.6.55-1_amd64.deb ... 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Setting up cpp-15-s390x-linux-gnu (15.2.0-13cross1) ... Setting up libtasn1-6:amd64 (4.21.0-2) ... Setting up fonts-lmodern (2.005-1) ... Setting up libopenjp2-7:amd64 (2.5.4-1) ... Setting up libx11-6:amd64 (2:1.8.12-1+b1) ... Setting up libthai-data (0.1.30-1) ... Setting up netbase (6.5) ... Setting up sgml-base (1.31+nmu1) ... Setting up libkrb5-3:amd64 (1.22.1-2) ... Setting up libicu76:amd64 (76.1-4+b1) ... Setting up libpaper2:amd64 (2.2.5-0.3+b3) ... Setting up gcc-15-cross-base (15.2.0-13cross1) ... Setting up libde265-0:amd64 (1.0.16-1+b1) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up gcc-15-base:s390x (15.2.0-13) ... Setting up libwebpmux3:amd64 (1.5.0-0.1+b1) ... Setting up readline-common (8.3-4) ... Setting up libgomp1-s390x-cross (15.2.0-13cross1) ... Setting up xdg-utils (1.2.1-2) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libsynctex2:amd64 (2025.20250727.75242+ds-5) ... 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Setting up libthai0:amd64 (0.1.30-1) ... Setting up libglib2.0-0t64:amd64 (2.87.2-3) ... No schema files found: doing nothing. Setting up libptexenc1:amd64 (2025.20250727.75242+ds-5) ... Setting up libfreetype6:amd64 (2.14.1+dfsg-2) ... Setting up libp11-kit0:amd64 (0.26.2-2) ... Setting up libgssapi-krb5-2:amd64 (1.22.1-2) ... Setting up libgcc-s1-s390x-cross (15.2.0-13cross1) ... Setting up ucf (3.0052) ... Setting up netpbm (2:11.13.03-1) ... Setting up libreadline8t64:amd64 (8.3-4) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up libitm1-s390x-cross (15.2.0-13cross1) ... Setting up liblqr-1-0:amd64 (0.4.2-2.2) ... Setting up groff-base (1.23.0-10) ... Setting up liblsan0-s390x-cross (15.2.0-13cross1) ... Setting up xml-core (0.19) ... Setting up libharfbuzz0b:amd64 (12.3.2-2) ... Setting up libsm6:amd64 (2:1.2.6-1+b1) ... Setting up libpython3.13-stdlib:amd64 (3.13.12-1) ... Setting up libavahi-client3:amd64 (0.8-18) ... Setting up libpython3-stdlib:amd64 (3.13.9-3) ... Setting up libgnutls30t64:amd64 (3.8.12-3) ... Setting up libxi6:amd64 (2:1.8.2-2) ... Setting up python3.13 (3.13.12-1) ... Setting up libgirepository-2.0-0:amd64 (2.87.2-3) ... Setting up libsombok3:amd64 (2.4.0-2+b3) ... Setting up libstdc++6-s390x-cross (15.2.0-13cross1) ... Setting up po-debconf (1.0.22) ... Setting up libglib2.0-bin (2.87.2-3) ... Setting up python3 (3.13.9-3) ... Setting up xfonts-utils (1:7.7+7) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libasan8-s390x-cross (15.2.0-13cross1) ... Setting up tex-common (6.20) ... update-language: texlive-base not installed and configured, doing nothing! Setting up python3-packaging (25.0-2) ... Setting up libunicode-linebreak-perl (0.0.20190101-3) ... Setting up libtsan2-s390x-cross (15.2.0-13cross1) ... Setting up libxt6t64:amd64 (1:1.2.1-1.3+b1) ... Setting up lmodern (2.005-1) ... Setting up libcups2t64:amd64 (2.4.16-1) ... Setting up libgio-2.0-dev-bin (2.87.2-3) ... Setting up libxmu6:amd64 (2:1.1.3-4) ... Setting up libubsan1-s390x-cross (15.2.0-13cross1) ... Setting up girepository-tools:amd64 (2.87.2-3) ... Setting up debhelper (13.30) ... Setting up libxaw7:amd64 (2:1.0.16-1+b1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up libgcc-15-dev-s390x-cross (15.2.0-13cross1) ... Setting up gcc-15-s390x-linux-gnu (15.2.0-13cross1) ... Setting up libgs10-common (10.06.0~dfsg-3) ... Setting up libglib2.0-dev-bin (2.87.2-3) ... Setting up fontconfig-config (2.17.1-5) ... Setting up libstdc++-15-dev-s390x-cross (15.2.0-13cross1) ... Setting up gcc-s390x-linux-gnu (4:15.2.0-5) ... Setting up libfontconfig1:amd64 (2.17.1-5) ... Setting up libgs10:amd64 (10.06.0~dfsg-3) ... Setting up g++-15-s390x-linux-gnu (15.2.0-13cross1) ... Setting up g++-s390x-linux-gnu (4:15.2.0-5) ... Setting up ghostscript (10.06.0~dfsg-3) ... Setting up libcairo2:amd64 (1.18.4-3) ... Setting up texlive-binaries (2025.20250727.75242+ds-5) ... 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 crossbuild-essential-s390x (12.12) ... Setting up texlive-base (2025.20260124-1) ... 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 texlive-luatex (2025.20260124-1) ... Setting up texlive-plain-generic (2025.20260124-1) ... Setting up texlive-latex-base (2025.20260124-1) ... Setting up texlive-extra-utils (2025.20260124-1) ... Setting up libheif-plugin-dav1d:amd64 (1.21.2-3) ... Setting up libheif-plugin-libde265:amd64 (1.21.2-3) ... Setting up libheif1:amd64 (1.21.2-3) ... Setting up libgcc-s1:s390x (15.2.0-13) ... Setting up libmagickcore-7.q16-10:amd64 (8:7.1.2.13+dfsg1-1) ... Setting up libc6:s390x (2.42-13) ... Setting up libffi8:s390x (3.5.2-3+b1) ... Setting up libasan8:s390x (15.2.0-13) ... Setting up libc6-dev:s390x (2.42-13) ... Setting up libtsan2:s390x (15.2.0-13) ... Setting up libblkid1:s390x (2.41.3-4) ... Setting up libstdc++6:s390x (15.2.0-13) ... Setting up liblsan0:s390x (15.2.0-13) ... Setting up libitm1:s390x (15.2.0-13) ... Setting up libmagickwand-7.q16-10:amd64 (8:7.1.2.13+dfsg1-1) ... Setting up zlib1g:s390x (1:1.3.dfsg+really1.3.1-3) ... Setting up libgomp1:s390x (15.2.0-13) ... Setting up libffi-dev:s390x (3.5.2-3+b1) ... Setting up libpcre2-16-0:s390x (10.46-1+b1) ... Setting up libpcre2-32-0:s390x (10.46-1+b1) ... Setting up libatomic1:s390x (15.2.0-13) ... Setting up libuuid1:s390x (2.41.3-4) ... Setting up libsepol2:s390x (3.9-2) ... Setting up libsepol-dev:s390x (3.9-2) ... Setting up libfl2:s390x (2.6.4-8.2+b5) ... Setting up libpcre2-8-0:s390x (10.46-1+b1) ... Setting up cross-exe-wrapper:s390x (0.2.6+b1) ... Setting up libubsan1:s390x (15.2.0-13) ... Setting up zlib1g-dev:s390x (1:1.3.dfsg+really1.3.1-3) ... Setting up libpcre2-posix3:s390x (10.46-1+b1) ... Setting up imagemagick-7.q16 (8:7.1.2.13+dfsg1-1) ... update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare (compare) in auto mode update-alternatives: using /usr/bin/compare-im7.q16 to provide /usr/bin/compare-im7 (compare-im7) in auto mode update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate (animate) in auto mode update-alternatives: using /usr/bin/animate-im7.q16 to provide /usr/bin/animate-im7 (animate-im7) in auto mode update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert (convert) in auto mode update-alternatives: using /usr/bin/convert-im7.q16 to provide /usr/bin/convert-im7 (convert-im7) in auto mode update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite (composite) in auto mode update-alternatives: using /usr/bin/composite-im7.q16 to provide /usr/bin/composite-im7 (composite-im7) in auto mode update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure (conjure) in auto mode update-alternatives: using /usr/bin/conjure-im7.q16 to provide /usr/bin/conjure-im7 (conjure-im7) in auto mode update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import (import) in auto mode update-alternatives: using /usr/bin/import-im7.q16 to provide /usr/bin/import-im7 (import-im7) in auto mode update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify (identify) in auto mode update-alternatives: using /usr/bin/identify-im7.q16 to provide /usr/bin/identify-im7 (identify-im7) in auto mode update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream (stream) in auto mode update-alternatives: using /usr/bin/stream-im7.q16 to provide /usr/bin/stream-im7 (stream-im7) in auto mode update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display (display) in auto mode update-alternatives: using /usr/bin/display-im7.q16 to provide /usr/bin/display-im7 (display-im7) in auto mode update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage (montage) in auto mode update-alternatives: using /usr/bin/montage-im7.q16 to provide /usr/bin/montage-im7 (montage-im7) in auto mode update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify (mogrify) in auto mode update-alternatives: using /usr/bin/mogrify-im7.q16 to provide /usr/bin/mogrify-im7 (mogrify-im7) in auto mode update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick (magick) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/magick.1.gz because associated file /usr/share/man/man1/magick-im7.q16.1.gz (of link group magick) does not exist update-alternatives: using /usr/bin/magick-im7.q16 to provide /usr/bin/magick-im7 (magick-im7) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/magick-im7.1.gz because associated file /usr/share/man/man1/magick-im7.q16.1.gz (of link group magick-im7) does not exist update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script (magick-script) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/magick-script.1.gz because associated file /usr/share/man/man1/magick-script-im7.q16.1.gz (of link group magick-script) does not exist update-alternatives: using /usr/bin/magick-script-im7.q16 to provide /usr/bin/magick-script-im7 (magick-script-im7) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/magick-script-im7.1.gz because associated file /usr/share/man/man1/magick-script-im7.q16.1.gz (of link group magick-script-im7) does not exist Setting up libgcc-15-dev:s390x (15.2.0-13) ... Setting up libpcre2-dev:s390x (10.46-1+b1) ... Setting up libfl-dev:s390x (2.6.4-8.2+b5) ... Setting up libselinux1:s390x (3.9-4+b1) ... Setting up libstdc++-15-dev:s390x (15.2.0-13) ... Setting up uuid-dev:s390x (2.41.3-4) ... Setting up hevea (2.36-2+b5) ... Setting up imagemagick (8:7.1.2.13+dfsg1-1) ... Setting up libmount1:s390x (2.41.3-4) ... Setting up libselinux-dev:s390x (3.9-4+b1) ... Setting up libblkid-dev:s390x (2.41.3-4) ... Setting up libglib2.0-0t64:s390x (2.87.2-3) ... /var/lib/dpkg/info/libglib2.0-0t64:s390x.postinst: 41: /usr/lib/s390x-linux-gnu/glib-2.0/glib-compile-schemas: Exec format error /var/lib/dpkg/info/libglib2.0-0t64:s390x.postinst: 42: /usr/lib/s390x-linux-gnu/glib-2.0/gio-querymodules: Exec format error Setting up libmount-dev:s390x (2.41.3-4) ... Setting up libgio-2.0-dev:s390x (2.87.2-3) ... Setting up libgirepository-2.0-0:s390x (2.87.2-3) ... Setting up girepository-tools:s390x (2.87.2-3) ... Setting up libglib2.0-dev:s390x (2.87.2-3) ... Processing triggers for libc-bin (2.42-13) ... Processing triggers for sgml-base (1.31+nmu1) ... Setting up sgml-data (2.0.11+nmu1) ... Processing triggers for sgml-base (1.31+nmu1) ... Setting up docbook (4.5-11) ... Processing triggers for sgml-base (1.31+nmu1) ... Setting up docbook-to-man (1:2.0.0-50) ... Setting up sbuild-build-depends-main-dummy:s390x (0.invalid.0) ... Processing triggers for tex-common (6.20) ... 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 (s390x included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.1.0-32-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.129-1 (2025-03-06) amd64 (x86_64) Toolchain package versions: binutils_2.46-2 dpkg-dev_1.23.5 g++-15_15.2.0-13 gcc-15_15.2.0-13 libc6-dev_2.42-13 libstdc++-15-dev_15.2.0-13 libstdc++-15-dev-s390x-cross_15.2.0-13cross1 libstdc++6_15.2.0-13 libstdc++6-s390x-cross_15.2.0-13cross1 linux-libc-dev_6.18.12-1 Package versions: apt_3.1.16 apt-utils_3.1.16 autoconf_2.72-3.1 automake_1:1.18.1-3 autopoint_0.23.2-1 autotools-dev_20240727.1 base-files_14 base-passwd_3.6.8 bash_5.3-2 binutils_2.46-2 binutils-common_2.46-2 binutils-s390x-linux-gnu_2.46-2 binutils-x86-64-linux-gnu_2.46-2 bsdextrautils_2.41.3-4 bsdutils_1:2.41.3-4 build-essential_12.12 bzip2_1.0.8-6+b1 coreutils_9.7-3 cpp_4:15.2.0-5 cpp-15_15.2.0-13 cpp-15-s390x-linux-gnu_15.2.0-13cross1 cpp-15-x86-64-linux-gnu_15.2.0-13 cpp-s390x-linux-gnu_4:15.2.0-5 cpp-x86-64-linux-gnu_4:15.2.0-5 cross-exe-wrapper_0.2.6+b1 crossbuild-essential-s390x_12.12 dash_0.5.12-12 debconf_1.5.92 debhelper_13.30 debian-archive-keyring_2025.1 debianutils_5.23.2 dh-autoreconf_21+nmu1 dh-strip-nondeterminism_1.15.0-1 diffutils_1:3.12-1 docbook_4.5-11 docbook-to-man_1:2.0.0-50 dpkg_1.23.5 dpkg-dev_1.23.5 dwz_0.16-2 fakeroot_1.37.2-1 file_1:5.46-5+b1 findutils_4.10.0-3 flex_2.6.4-8.2+b5 fontconfig-config_2.17.1-5 fonts-lmodern_2.005-1 fonts-urw-base35_20200910-8 g++_4:15.2.0-5 g++-15_15.2.0-13 g++-15-s390x-linux-gnu_15.2.0-13cross1 g++-15-x86-64-linux-gnu_15.2.0-13 g++-s390x-linux-gnu_4:15.2.0-5 g++-x86-64-linux-gnu_4:15.2.0-5 gcc_4:15.2.0-5 gcc-15_15.2.0-13 gcc-15-base_15.2.0-13 gcc-15-cross-base_15.2.0-13cross1 gcc-15-s390x-linux-gnu_15.2.0-13cross1 gcc-15-s390x-linux-gnu-base_15.2.0-13cross1 gcc-15-x86-64-linux-gnu_15.2.0-13 gcc-s390x-linux-gnu_4:15.2.0-5 gcc-x86-64-linux-gnu_4:15.2.0-5 gettext_0.23.2-1 gettext-base_0.23.2-1 ghostscript_10.06.0~dfsg-3 girepository-tools_2.87.2-3 grep_3.12-1 groff-base_1.23.0-10 gzip_1.13-1 hevea_2.36-2+b5 hicolor-icon-theme_0.18-2 hostname_3.25 imagemagick_8:7.1.2.13+dfsg1-1 imagemagick-7-common_8:7.1.2.13+dfsg1-1 imagemagick-7.q16_8:7.1.2.13+dfsg1-1 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-3 libapt-pkg7.0_3.1.16 libarchive-zip-perl_1.68-1 libasan8_15.2.0-13 libasan8-s390x-cross_15.2.0-13cross1 libatomic1_15.2.0-13 libatomic1-s390x-cross_15.2.0-13cross1 libattr1_1:2.5.2-4 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b1 libavahi-client3_0.8-18 libavahi-common-data_0.8-18 libavahi-common3_0.8-18 libbinutils_2.46-2 libblkid-dev_2.41.3-4 libblkid1_2.41.3-4 libbrotli1_1.2.0-3 libbsd0_0.12.2-2+b1 libbz2-1.0_1.0.8-6+b1 libc-bin_2.42-13 libc-dev-bin_2.42-13 libc-gconv-modules-extra_2.42-13 libc6_2.42-13 libc6-dev_2.42-13 libc6-dev-s390x-cross_2.42-12cross1 libc6-s390x-cross_2.42-12cross1 libcairo2_1.18.4-3 libcap-ng0_0.9.1-1 libcap2_1:2.75-10+b5 libcc1-0_15.2.0-13 libcom-err2_1.47.2-3+b8 libcrypt1_1:4.5.1-1 libctf-nobfd0_2.46-2 libctf0_2.46-2 libcups2t64_2.4.16-1 libdatrie1_0.2.14-1 libdav1d7_1.5.3-1+b1 libdb5.3t64_5.3.28+dfsg2-11 libdbus-1-3_1.16.2-3 libde265-0_1.0.16-1+b1 libdebconfclient0_0.282+b2 libdebhelper-perl_13.30 libdeflate0_1.23-2+b1 libdpkg-perl_1.23.5 libelf1t64_0.194-1 libexpat1_2.7.4-1 libfakeroot_1.37.2-1 libffi-dev_3.5.2-3+b1 libffi8_3.5.2-3+b1 libfftw3-double3_3.3.10-2+b2 libfile-homedir-perl_1.006-2 libfile-stripnondeterminism-perl_1.15.0-1 libfile-which-perl_1.27-2 libfl-dev_2.6.4-8.2+b5 libfl2_2.6.4-8.2+b5 libfontconfig1_2.17.1-5 libfontenc1_1:1.1.8-1+b3 libfreetype6_2.14.1+dfsg-2 libgcc-15-dev_15.2.0-13 libgcc-15-dev-s390x-cross_15.2.0-13cross1 libgcc-s1_15.2.0-13 libgcc-s1-s390x-cross_15.2.0-13cross1 libgdbm-compat4t64_1.26-1+b1 libgdbm6t64_1.26-1+b1 libgio-2.0-dev_2.87.2-3 libgio-2.0-dev-bin_2.87.2-3 libgirepository-2.0-0_2.87.2-3 libglib2.0-0t64_2.87.2-3 libglib2.0-bin_2.87.2-3 libglib2.0-data_2.87.2-3 libglib2.0-dev_2.87.2-3 libglib2.0-dev-bin_2.87.2-3 libgmp10_2:6.3.0+dfsg-5+b1 libgnutls30t64_3.8.12-3 libgomp1_15.2.0-13 libgomp1-s390x-cross_15.2.0-13cross1 libgprofng0_2.46-2 libgraphite2-3_1.3.14-11+b1 libgs-common_10.06.0~dfsg-3 libgs10_10.06.0~dfsg-3 libgs10-common_10.06.0~dfsg-3 libgssapi-krb5-2_1.22.1-2 libharfbuzz0b_12.3.2-2 libheif-plugin-dav1d_1.21.2-3 libheif-plugin-libde265_1.21.2-3 libheif1_1.21.2-3 libhogweed6t64_3.10.2-1 libhwasan0_15.2.0-13 libice6_2:1.1.1-1+b1 libicu76_76.1-4+b1 libidn12_1.43-2+b1 libidn2-0_2.3.8-4+b1 libijs-0.35_0.35-16+b1 libisl23_0.27-1+b1 libitm1_15.2.0-13 libitm1-s390x-cross_15.2.0-13cross1 libjansson4_2.14-2+b4 libjbig0_2.1-6.1+b3 libjbig2dec0_0.20-1+b4 libjpeg62-turbo_1:2.1.5-4 libk5crypto3_1.22.1-2 libkeyutils1_1.6.3-6+b1 libkpathsea6_2025.20250727.75242+ds-5 libkrb5-3_1.22.1-2 libkrb5support0_1.22.1-2 liblcms2-2_2.17-1 liblerc4_4.0.0+ds-5+b1 liblqr-1-0_0.4.2-2.2 liblsan0_15.2.0-13 liblsan0-s390x-cross_15.2.0-13cross1 libltdl7_2.5.4-9 liblz4-1_1.10.0-6 liblzma5_5.8.2-2 libmagic-mgc_1:5.46-5+b1 libmagic1t64_1:5.46-5+b1 libmagickcore-7.q16-10_8:7.1.2.13+dfsg1-1 libmagickwand-7.q16-10_8:7.1.2.13+dfsg1-1 libmd0_1.1.0-2+b2 libmime-charset-perl_1.013.1-2 libmount-dev_2.41.3-4 libmount1_2.41.3-4 libmpc3_1.3.1-2+b1 libmpfi0_1.5.4+ds-4+b1 libmpfr6_4.2.2-2+b1 libncursesw6_6.6+20251231-1 libnetpbm11t64_2:11.13.03-1 libnettle8t64_3.10.2-1 libopenjp2-7_2.5.4-1 libosp5_1.5.2-15.2 libp11-kit0_0.26.2-2 libpam-modules_1.7.0-5+b1 libpam-modules-bin_1.7.0-5+b1 libpam-runtime_1.7.0-5 libpam0g_1.7.0-5+b1 libpaper-utils_2.2.5-0.3+b3 libpaper2_2.2.5-0.3+b3 libpcre2-16-0_10.46-1+b1 libpcre2-32-0_10.46-1+b1 libpcre2-8-0_10.46-1+b1 libpcre2-dev_10.46-1+b1 libpcre2-posix3_10.46-1+b1 libperl5.40_5.40.1-7 libpipeline1_1.5.8-2 libpixman-1-0_0.46.4-1+b1 libpkgconf7_2.5.1-4 libpng16-16t64_1.6.55-1 libpotrace0_1.16-2+b3 libproc2-0_2:4.0.4-9+b1 libptexenc1_2025.20250727.75242+ds-5 libpython3-stdlib_3.13.9-3 libpython3.13-minimal_3.13.12-1 libpython3.13-stdlib_3.13.12-1 libquadmath0_15.2.0-13 libraw23t64_0.21.5b-1 libreadline8t64_8.3-4 libseccomp2_2.6.0-2+b1 libselinux-dev_3.9-4+b1 libselinux1_3.9-4+b1 libsemanage-common_3.9-1 libsemanage2_3.9-1+b1 libsepol-dev_3.9-2 libsepol2_3.9-2 libsframe3_2.46-2 libsharpyuv0_1.5.0-0.1+b1 libsm6_2:1.2.6-1+b1 libsmartcols1_2.41.3-4 libsombok3_2.4.0-2+b3 libsqlite3-0_3.46.1-9 libssl3t64_3.5.5-1 libstdc++-15-dev_15.2.0-13 libstdc++-15-dev-s390x-cross_15.2.0-13cross1 libstdc++6_15.2.0-13 libstdc++6-s390x-cross_15.2.0-13cross1 libsynctex2_2025.20250727.75242+ds-5 libsysprof-capture-4-dev_50~beta-1 libsystemd0_259.1-1 libtasn1-6_4.21.0-2 libteckit0_2.5.13+ds-1 libtexlua53-5_2025.20250727.75242+ds-5 libtext-charwidth-perl_0.04-11+b5 libtext-wrapi18n-perl_0.06-10 libthai-data_0.1.30-1 libthai0_0.1.30-1 libtiff6_4.7.1-1 libtinfo6_6.6+20251231-1 libtool_2.5.4-9 libtsan2_15.2.0-13 libtsan2-s390x-cross_15.2.0-13cross1 libubsan1_15.2.0-13 libubsan1-s390x-cross_15.2.0-13cross1 libuchardet0_0.0.8-2+b1 libudev1_259.1-1 libunicode-linebreak-perl_0.0.20190101-3 libunistring5_1.3-2+b1 libuuid1_2.41.3-4 libwebp7_1.5.0-0.1+b1 libwebpdemux2_1.5.0-0.1+b1 libwebpmux3_1.5.0-0.1+b1 libx11-6_2:1.8.12-1+b1 libx11-data_2:1.8.12-1 libxau6_1:1.0.11-1+b1 libxaw7_2:1.0.16-1+b1 libxcb-render0_1.17.0-2+b2 libxcb-shm0_1.17.0-2+b2 libxcb1_1.17.0-2+b2 libxdmcp6_1:1.1.5-2 libxext6_2:1.3.4-1+b4 libxi6_2:1.8.2-2 libxml2-16_2.15.1+dfsg-2+b1 libxmu6_2:1.1.3-4 libxpm4_1:3.5.17-1+b4 libxrender1_1:0.9.12-1+b1 libxt6t64_1:1.2.1-1.3+b1 libxxhash0_0.8.3-2+b1 libyaml-tiny-perl_1.76-1 libzstd1_1.5.7+dfsg-3+b1 libzzip-0-13t64_0.13.78+dfsg.1-0.2 linux-libc-dev_6.18.12-1 linux-libc-dev-s390x-cross_6.18.12-1 lmodern_2.005-1 login_1:4.16.0-2+really2.41.3-4 login.defs_1:4.19.2-1 m4_1.4.21-1 make_4.4.1-3 man-db_2.13.1-1 mawk_1.3.4.20260129-1 media-types_14.0.0 mount_2.41.3-4 native-architecture_0.2.6 ncurses-base_6.6+20251231-1 ncurses-bin_6.6+20251231-1 netbase_6.5 netpbm_2:11.13.03-1 opensp_1.5.2-15.2 openssl-provider-legacy_3.5.5-1 passwd_1:4.19.2-1 patch_2.8-2 perl_5.40.1-7 perl-base_5.40.1-7 perl-modules-5.40_5.40.1-7 pkgconf_2.5.1-4 pkgconf-bin_2.5.1-4 po-debconf_1.0.22 poppler-data_0.4.12-1 procps_2:4.0.4-9+b1 python3_3.13.9-3 python3-minimal_3.13.9-3 python3-packaging_25.0-2 python3.13_3.13.12-1 python3.13-minimal_3.13.12-1 qemu-user_1:10.2.1+ds-1 readline-common_8.3-4 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.26 sgml-base_1.31+nmu1 sgml-data_2.0.11+nmu1 sqv_1.3.0-5 sysvinit-utils_3.15-6 t1utils_1.41-4 tar_1.35+dfsg-4 tex-common_6.20 texlive-base_2025.20260124-1 texlive-binaries_2025.20250727.75242+ds-5 texlive-extra-utils_2025.20260124-1 texlive-latex-base_2025.20260124-1 texlive-luatex_2025.20260124-1 texlive-plain-generic_2025.20260124-1 tzdata_2025c-3 ucf_3.0052 util-linux_2.41.3-4 uuid-dev_2.41.3-4 x11-common_1:7.7+26 xdg-utils_1.2.1-2 xfonts-encodings_1:1.0.4-2.2 xfonts-utils_1:7.7+7 xml-core_0.19 xz-utils_5.8.2-2 zlib1g_1:1.3.dfsg+really1.3.1-3 zlib1g-dev_1:1.3.dfsg+really1.3.1-3 +------------------------------------------------------------------------------+ | 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: 2.4.1-28 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Charles Plessy , Andreas Tille Homepage: https://www.ebi.ac.uk/~birney/wise2/ Standards-Version: 4.7.3 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 (= 13), texlive-latex-base, texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev, libfl-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 41874d798085658bfd41d252ee306400fef91ad6 42224 wise_2.4.1-28.debian.tar.xz Checksums-Sha256: 0aec5e30739110783517a429606249fc6c5fd0d65171c1a6d79ecc5ff81d2935 3410178 wise_2.4.1.orig.tar.gz 2286137047eaf08e27e313548503eb3d56bbdb90ad35dbd85f967201f33c6a54 42224 wise_2.4.1-28.debian.tar.xz Files: 9e90132c19a653831ce63b5af7f08302 3410178 wise_2.4.1.orig.tar.gz 906f176e08a0a15e1aec1d27d5c67a87 42224 wise_2.4.1-28.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQEzBAEBCgAdFiEE1Uw7+v+wQt44LaXXQc5/C58bizIFAmmYLfgACgkQQc5/C58b izLKLQf/c0Hj2/8ehzFxmgFH1AYEt76dbOldc1JnMlRz2ZDYpiSP2Wa1ZI/HGXsp h79K7ZayKE5RgGl3YGx4Fp1PwvKh5ApT47m0CoDYhmfobP93ErWt1GHyidOWYePk PS/dbmR4TxDvBI1mlTM7y7hSomrtYr+4pl6urlXLFQxHEUDBJWmUzlRGM4zls5l2 qICtkwRlAbxPwqCjnmMDOYNMQF4KpGxRyb9jdxGLyTlEfAsU2wr4S7zugHabC5zh /jWJLaZs3zqcLha2AvdyqQpRrjhuNV3FMCJ7avAN9EESl1jJbjbUb+v/BWgKx1cM PEDY5eBJws1e8J4dKSeD/s48nJ/aKQ== =HR+E -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./wise_2.4.1-28.dsc: missing OpenPGP keyrings dpkg-source: info: verifying ./wise_2.4.1-28.dsc dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-keyring.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-tag2upload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-nonupload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-maintainers.pgp dpkg-source: info: extracting wise in /<> dpkg-source: info: unpacking wise_2.4.1.orig.tar.gz dpkg-source: info: unpacking wise_2.4.1-28.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 dpkg-source: info: applying implicit-function-declaration.patch dpkg-source: info: applying executable-is-script.patch dpkg-source: info: applying gcc-14.patch dpkg-source: info: applying fix_blhc.patch dpkg-source: info: applying fix_ftbfs_with_gcc-15.patch dpkg-source: info: applying side-effects.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.s390x 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.1zZwpEFM0s/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-19e3abce-58a6-4182-9f82-36ef7f2390f2 SCHROOT_UID=1000 SCHROOT_USER=crossqa SHELL=/bin/sh USER=crossqa XDG_SESSION_CLASS=user dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -as390x -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package wise dpkg-buildpackage: info: source version 2.4.1-28 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Santiago Vila dpkg-architecture: warning: specified GNU system type s390x-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 s390x 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 \( -name autom4te.cache -o -name __pycache__ \) -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 '/<>' # The dyc compiler is needed before building the all the rest. # Also, it pre-depends on the libwisebase library, otherwise # linking fails. dh_auto_build --sourcedirectory=src/base -- libwisebase.a cd src/base && make -j1 INSTALL="install --strip-program=true" PKG_CONFIG=s390x-linux-gnu-pkg-config CXX=s390x-linux-gnu-g\+\+ CC=s390x-linux-gnu-gcc libwisebase.a make[2]: Entering directory '/<>/src/base' s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wiseconfig.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wisestring.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wiseerror.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wisememman.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread 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 * s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wiserandom.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wisetime.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wiseoverlay.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wisestreaminterface.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread commandline.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread 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[2]: Leaving directory '/<>/src/base' dh_auto_build --sourcedirectory=src/dyc -- dyc cd src/dyc && make -j1 INSTALL="install --strip-program=true" PKG_CONFIG=s390x-linux-gnu-pkg-config CXX=s390x-linux-gnu-g\+\+ CC=s390x-linux-gnu-gcc dyc make[2]: Entering directory '/<>/src/dyc' s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ dyc.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ dyna2.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ dynfile.c dynfile.dy: In function ‘warn_expr’: dynfile.dy:699:16: warning: ‘%s’ directive writing up to 511 bytes into a region of size 506 [-Wformat-overflow=] 699 | sprintf(buf2,"warn(\"%s\");",buffer); | ^~~~~~~~~~~~~~~ ~~~~~~ In file included from /usr/s390x-linux-gnu/include/stdio.h:970, from ../base/wisebase.h:6, from dynfile.h:6, from dynfile.c:4: In function ‘sprintf’, inlined from ‘warn_expr’ at dynfile.dy:699:3: /usr/s390x-linux-gnu/include/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 10 and 521 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 ()); | ~~~~~~~~~~~~~~~~~ s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ wisec.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ dynafunc.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ module.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ type.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ method.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ dynadb.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ friend.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ inputfile.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ variable.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ modulefunc.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ api.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ display.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ dynashadow.c dynashadow.dy: In function ‘optimised_shadow_GenericMatrix’: dynashadow.dy:2180:31: warning: passing argument 2 of ‘write_main_shadow_block’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2180 | write_main_shadow_block(dfp,gm,"DC_OPT_SHADOW_MATRIX","mat","DC_OPT_SHADOW_SPECIAL","DC_OPT_SHADOW_MATRIX_SP","DC_OPT_SHADOW_SPECIAL_SP",7,TRUE,TRUE,0,TRUE); | ^~ In file included from dynashadow.c:4: dynashadow.h:163:60: note: expected ‘GenericMatrix *’ but argument is of type ‘const GenericMatrix *’ 163 | void write_main_shadow_block(DYNFILE * dfp,GenericMatrix * gm,char * matrixtag,char * pointer_tag,char * specialtag,char * shadow_main_tag,char * shadow_special_tag,int shadow_length,boolean shadow_on_special,boolean use_special,int debug,int use_shadow_pointer); | ~~~~~~~~~~~~~~~~^~ dynashadow.dy:2187:36: warning: passing argument 2 of ‘write_special_shadow_block’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 2187 | write_special_shadow_block(dfp,gm,"DC_OPT_SHADOW_MATRIX","mat","DC_OPT_SHADOW_SPECIAL","DC_OPT_SHADOW_MATRIX_SP","DC_OPT_SHADOW_SPECIAL_SP",7,TRUE,0); | ^~ dynashadow.h:189:63: note: expected ‘GenericMatrix *’ but argument is of type ‘const GenericMatrix *’ 189 | void write_special_shadow_block(DYNFILE * dfp,GenericMatrix * gm,char * matrix,char * pointer_tag,char * special,char * shadow_main_tag,char * shadow_special_tag,int shadow_length,boolean shadow_on_special,int debug); | ~~~~~~~~~~~~~~~~^~ s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ labelmaster.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ ftext.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ funcinfo.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ objectinfo.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ exprtree.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ compugen.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ docugen.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ input.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ dpimpl.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ dbthread.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ probal.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ telegraph.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ dynadebug.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ dyshatter.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ y.tab.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g -DUNIX -I../base/ -I../base/ lex.yy.c s390x-linux-gnu-gcc -o dyc dyc.o dyna2.o dynfile.o wisec.o dynafunc.o module.o type.o method.o dynadb.o friend.o inputfile.o variable.o modulefunc.o api.o display.o dynashadow.o labelmaster.o ftext.o funcinfo.o objectinfo.o exprtree.o compugen.o docugen.o input.o dpimpl.o dbthread.o probal.o telegraph.o dynadebug.o dyshatter.o y.tab.o lex.yy.o -ll -lwisebase -Wl,-z,relro -Wl,-z,now -g -lm -L../base/ -lpthread make[2]: Leaving directory '/<>/src/dyc' PATH="$PATH:/<>/src/dyc" \ dh_auto_build --sourcedirectory=src -- all cd src && make -j1 INSTALL="install --strip-program=true" PKG_CONFIG=s390x-linux-gnu-pkg-config CXX=s390x-linux-gnu-g\+\+ CC=s390x-linux-gnu-gcc all make[2]: Entering directory '/<>/src' (cd base ; make CC="s390x-linux-gnu-gcc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c `s390x-linux-gnu-pkg-config --cflags glib-2.0`" libwisebase.a ) make[3]: Entering directory '/<>/src/base' make[3]: 'libwisebase.a' is up to date. make[3]: Leaving directory '/<>/src/base' (cd HMMer2 ; make CC="s390x-linux-gnu-gcc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c `s390x-linux-gnu-pkg-config --cflags glib-2.0`" libhmmer.a ) make[3]: Entering directory '/<>/src/HMMer2' s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c alphabet.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c core_algorithms.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c debug.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c emit.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c emulation.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c histogram.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c hmmio.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c mathsupport.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c masks.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c misc.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c modelmakers.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c plan7.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c plan9.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c prior.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c tophits.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c trace.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c aligneval.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c alignio.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c cluster.c cluster.c: In function ‘Cluster’: cluster.c:178:26: warning: argument 1 range [18446744065119617024, 18446744073709551612] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 178 | (diff = (float *) malloc ((N-1) * sizeof(float))) == NULL) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from squid.h:22, from cluster.c:122: /usr/s390x-linux-gnu/include/stdlib.h:672:14: note: in a call to allocation function ‘malloc’ declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^~~~~~ s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c dayhoff.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c file.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c getopt.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c gnuregex.c gnuregex.c: In function ‘re_set_syntax’: gnuregex.c:795:1: warning: old-style function definition [-Wold-style-definition] 795 | re_set_syntax (syntax) | ^~~~~~~~~~~~~ gnuregex.c: In function ‘regex_compile’: gnuregex.c:1050:1: warning: old-style function definition [-Wold-style-definition] 1050 | regex_compile (pattern, size, syntax, bufp) | ^~~~~~~~~~~~~ gnuregex.c: In function ‘store_op1’: gnuregex.c:2051:1: warning: old-style function definition [-Wold-style-definition] 2051 | store_op1 (op, loc, arg) | ^~~~~~~~~ gnuregex.c: In function ‘store_op2’: gnuregex.c:2064:1: warning: old-style function definition [-Wold-style-definition] 2064 | store_op2 (op, loc, arg1, arg2) | ^~~~~~~~~ gnuregex.c: In function ‘insert_op1’: gnuregex.c:2079:1: warning: old-style function definition [-Wold-style-definition] 2079 | insert_op1 (op, loc, arg, end) | ^~~~~~~~~~ gnuregex.c: In function ‘insert_op2’: gnuregex.c:2098:1: warning: old-style function definition [-Wold-style-definition] 2098 | insert_op2 (op, loc, arg1, arg2, end) | ^~~~~~~~~~ gnuregex.c: In function ‘at_begline_loc_p’: gnuregex.c:2119:1: warning: old-style function definition [-Wold-style-definition] 2119 | at_begline_loc_p (pattern, p, syntax) | ^~~~~~~~~~~~~~~~ gnuregex.c: In function ‘at_endline_loc_p’: gnuregex.c:2138:1: warning: old-style function definition [-Wold-style-definition] 2138 | at_endline_loc_p (p, pend, syntax) | ^~~~~~~~~~~~~~~~ gnuregex.c: In function ‘group_in_compile_stack’: gnuregex.c:2160:1: warning: old-style function definition [-Wold-style-definition] 2160 | group_in_compile_stack (compile_stack, regnum) | ^~~~~~~~~~~~~~~~~~~~~~ gnuregex.c: In function ‘compile_range’: gnuregex.c:2188:1: warning: old-style function definition [-Wold-style-definition] 2188 | compile_range (p_ptr, pend, translate, syntax, b) | ^~~~~~~~~~~~~ gnuregex.c: In function ‘re_compile_fastmap’: gnuregex.c:2520:1: warning: old-style function definition [-Wold-style-definition] 2520 | re_compile_fastmap (bufp) | ^~~~~~~~~~~~~~~~~~ gnuregex.c: In function ‘re_set_registers’: gnuregex.c:2805:1: warning: old-style function definition [-Wold-style-definition] 2805 | re_set_registers (bufp, regs, num_regs, starts, ends) | ^~~~~~~~~~~~~~~~ gnuregex.c: In function ‘re_search’: gnuregex.c:2832:1: warning: old-style function definition [-Wold-style-definition] 2832 | re_search (bufp, string, size, startpos, range, regs) | ^~~~~~~~~ gnuregex.c: In function ‘re_search_2’: gnuregex.c:2865:1: warning: old-style function definition [-Wold-style-definition] 2865 | re_search_2 (bufp, string1, size1, string2, size2, startpos, range, regs, stop) | ^~~~~~~~~~~ gnuregex.c: In function ‘re_match’: gnuregex.c:3126:1: warning: old-style function definition [-Wold-style-definition] 3126 | re_match (bufp, string, size, pos, regs) | ^~~~~~~~ gnuregex.c: In function ‘re_match_2’: gnuregex.c:3151:1: warning: old-style function definition [-Wold-style-definition] 3151 | re_match_2 (bufp, string1, size1, string2, size2, pos, regs, stop) | ^~~~~~~~~~ gnuregex.c:3755:31: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 3755 | if ((int) old_regend[r] >= (int) regstart[r]) | ^ gnuregex.c:3755:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 3755 | if ((int) old_regend[r] >= (int) regstart[r]) | ^ gnuregex.c:2316:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2316 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2395:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2395 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3761:19: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3761 | PUSH_FAILURE_POINT (p1 + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2316:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2316 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2398:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2398 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3761:19: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3761 | PUSH_FAILURE_POINT (p1 + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2316:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2316 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2395:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2395 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3908:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3908 | PUSH_FAILURE_POINT (p + mcnt, NULL, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2316:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2316 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2398:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2398 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3908:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3908 | PUSH_FAILURE_POINT (p + mcnt, NULL, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2316:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2316 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2395:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2395 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3961:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3961 | PUSH_FAILURE_POINT (p + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2316:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2316 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2398:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2398 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:3961:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 3961 | PUSH_FAILURE_POINT (p + mcnt, d, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2483:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2483 | high_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^ gnuregex.c:4067:13: note: in expansion of macro ‘POP_FAILURE_POINT’ 4067 | POP_FAILURE_POINT (sdummy, pdummy, | ^~~~~~~~~~~~~~~~~ gnuregex.c:2486:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2486 | low_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^ gnuregex.c:4067:13: note: in expansion of macro ‘POP_FAILURE_POINT’ 4067 | POP_FAILURE_POINT (sdummy, pdummy, | ^~~~~~~~~~~~~~~~~ gnuregex.c:2316:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2316 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2395:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2395 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:4100:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 4100 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2316:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2316 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2398:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2398 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:4100:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 4100 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2316:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2316 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2395:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2395 | PUSH_FAILURE_ITEM (lowest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:4113:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 4113 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2316:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] 2316 | fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item | ^ gnuregex.c:2398:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’ 2398 | PUSH_FAILURE_ITEM (highest_active_reg); \ | ^~~~~~~~~~~~~~~~~ gnuregex.c:4113:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’ 4113 | PUSH_FAILURE_POINT (0, 0, -2); | ^~~~~~~~~~~~~~~~~~ gnuregex.c:2483:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2483 | high_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^ gnuregex.c:4281:11: note: in expansion of macro ‘POP_FAILURE_POINT’ 4281 | POP_FAILURE_POINT (d, p, | ^~~~~~~~~~~~~~~~~ gnuregex.c:2486:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] 2486 | low_reg = (unsigned) POP_FAILURE_ITEM (); \ | ^ gnuregex.c:4281:11: note: in expansion of macro ‘POP_FAILURE_POINT’ 4281 | POP_FAILURE_POINT (d, p, | ^~~~~~~~~~~~~~~~~ gnuregex.c: In function ‘group_match_null_string_p’: gnuregex.c:4347:1: warning: old-style function definition [-Wold-style-definition] 4347 | group_match_null_string_p (p, end, reg_info) | ^~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c: In function ‘alt_match_null_string_p’: gnuregex.c:4456:1: warning: old-style function definition [-Wold-style-definition] 4456 | alt_match_null_string_p (p, end, reg_info) | ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c: In function ‘common_op_match_null_string_p’: gnuregex.c:4493:1: warning: old-style function definition [-Wold-style-definition] 4493 | common_op_match_null_string_p (p, end, reg_info) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c: In function ‘bcmp_translate’: gnuregex.c:4581:1: warning: old-style function definition [-Wold-style-definition] 4581 | bcmp_translate (s1, s2, len, translate) | ^~~~~~~~~~~~~~ gnuregex.c: In function ‘regcomp’: gnuregex.c:4723:1: warning: old-style function definition [-Wold-style-definition] 4723 | regcomp (preg, pattern, cflags) | ^~~~~~~ gnuregex.c: In function ‘regexec’: gnuregex.c:4798:1: warning: old-style function definition [-Wold-style-definition] 4798 | regexec (preg, string, nmatch, pmatch, eflags) | ^~~~~~~ gnuregex.c: In function ‘regerror’: gnuregex.c:4863:1: warning: old-style function definition [-Wold-style-definition] 4863 | regerror (errcode, preg, errbuf, errbuf_size) | ^~~~~~~~ gnuregex.c: In function ‘regfree’: gnuregex.c:4907:1: warning: old-style function definition [-Wold-style-definition] 4907 | regfree (preg) | ^~~~~~~ s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c interleaved.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c iupac.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c msf.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c revcomp.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c selex.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c sqerror.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c sqio.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c sre_ctype.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c sre_math.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c sre_string.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c stack.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c translate.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -c types.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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="s390x-linux-gnu-gcc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c `s390x-linux-gnu-pkg-config --cflags glib-2.0`" libdyna.a ) make[3]: Entering directory '/<>/src/dynlibsrc' s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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); | ^~~~~~~~~~~~~~~~~~~~~~~~~ s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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); | ^~~~~~~~~~~~ s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ dnamatrix.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ probability.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ alnrange.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ alnconvert.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ basematrix.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ shattermatrix.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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); | ^~~~~~~~~~~~~~~~~~~~~~~~ s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ dpenvelope.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ dbsearchimpl.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ dprunimpl.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ complexsequence.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ complexevalset.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ complexconsensi.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ sequence.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ sequencestream.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ seqalign.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hitlist.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hsp.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hspstream.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ codon.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ compmat.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ codonmatrix.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ codonmapper.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ sequencedb.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hscore.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ seqlookup.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ arrayseqlookup.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ genericindexresult.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ linkedlist_lookpos.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ singlenumberspace.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ histogram.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ searchstatinterface.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ searchstatlookup.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ proteindb.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ protein.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ pairbase.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ pairbaseseq.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ genomicdb.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ randommodel.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ randomdb.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ genomic.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ cdna.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ cdnadb.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ dna.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ embl.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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); | ^~~~~~~~~~~~~~~~~~~~~~~~ s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ gene.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ transcript.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ translation.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ btcanvas.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ asciibtcanvas.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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="s390x-linux-gnu-gcc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c `s390x-linux-gnu-pkg-config --cflags glib-2.0`" libdyna_glib.a ) make[3]: Entering directory '/<>/src/dynlibsrc' s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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); | ^ s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ intallocator.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ proteinstreamedindex.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ shadowseq.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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 s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hsphandler.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hspscaninterface.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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} s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hsplookupscan.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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 s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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 * s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hspscanruntime.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hsptwohitscan.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ proteinindexcons.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ dnaindexcons.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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="s390x-linux-gnu-gcc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c `s390x-linux-gnu-pkg-config --cflags glib-2.0`" all ) make[3]: Entering directory '/<>/src/external' (cd mott; make CC="s390x-linux-gnu-gcc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread" all) make[4]: Entering directory '/<>/src/external/mott' s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mott_api.o mott_api.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -c -o gaplib.o gaplib.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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="s390x-linux-gnu-gcc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c `s390x-linux-gnu-pkg-config --cflags glib-2.0`" libwisesocket.a ) make[3]: Entering directory '/<>/src/socket' s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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); | ^~~~~~~~~~~~~~~~~~~~~~~ s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ functionclient.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ anonobj.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ transferinterface.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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="s390x-linux-gnu-gcc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c `s390x-linux-gnu-pkg-config --cflags glib-2.0`" all ) make[3]: Entering directory '/<>/src/dnaindex' s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models kmer_index_interface.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models kmer_direct.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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} s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models kmer_count.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models kmer_glib_index.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models singleseqspace.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models dnamapping.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models largeseqreader.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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: In function ‘Wise2_lift_forward_tangled_KmerAssemblyPath’: kmer_assembly_untangler.dy:753:20: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 6 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 753 | 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:753:20: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 8 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=] 753 | 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} s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_contig.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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 * s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models assembly.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models compressed_protein_index.c make[3]: Leaving directory '/<>/src/dnaindex' (cd network ; make CC="s390x-linux-gnu-gcc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c `s390x-linux-gnu-pkg-config --cflags glib-2.0`" all ) make[3]: Entering directory '/<>/src/network' s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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); | ^~~~~~~~~~~~ s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../socket -I../dynlibsrc -I../dnaindex net_hspscan.c s390x-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 `s390x-linux-gnu-pkg-config --libs glib-2.0` -lpthread s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../socket -I../dynlibsrc -I../dnaindex client_multihspscan.c make[3]: Leaving directory '/<>/src/network' (cd models ; make CC="s390x-linux-gnu-gcc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c `s390x-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' s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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); | ^~~~~~~~~~~~ s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ dnaalign.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ seqaligndisplay.c s390x-linux-gnu-gcc -o dnal dnal.o dnaalign.o seqaligndisplay.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `s390x-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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); | ^~~~~~~~~~~~ s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ proteinsw.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ sw_wrap.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ abc.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ pba.c s390x-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 `s390x-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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); | ^~~~~~~~~~~~ s390x-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 `s390x-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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 s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ dba.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ slimdba.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ bigdba.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ dbadisplay.c s390x-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 `s390x-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread 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); | ^~~~~~~~~~~~ s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneparser21.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneparameter.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genestats.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genewisehsp.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneutil.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneoutput.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ threestatemodel.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genefrequency.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ splicesitemodeler.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genewise4.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genewise6.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genestretch6.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genewise21.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneloop21.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneloop6.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genephase6.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ gwlite.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ gwlitemodel.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ gwrap.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ matchsum.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estwrap.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genewisemodel.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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/s390x-linux-gnu/include/stdio.h:970, 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/s390x-linux-gnu/include/bits/stdio2.h:305:1: note: in a call to function ‘fgets’ declared with attribute ‘access (write_only, 1, 2)’ 305 | fgets (__fortify_clang_overload_arg (char *, __restrict, __s), int __n, | ^~~~~ In function ‘fgets’, inlined from ‘Wise2_read_fasta_PhasedProtein’ at phasemodel.dy:241:3: /usr/s390x-linux-gnu/include/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ cdparser.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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); | ^~~~~~~~~~~~~~~~ s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estwise3.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estslim3.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estloop3.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estfrag3.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estslimloop.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ gwquickdb.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ threestatedb.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ pfamhmmer1db.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ pwmdna.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../HMMer2/ -DHMMER_INTERNAL -I../base/ -I../dynlibsrc/ wise2xhmmer2.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genewisemodeldb.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ seqhit.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ standardout.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneparser4.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estquick3.c s390x-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 `s390x-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 `s390x-linux-gnu-pkg-config --libs glib-2.0` s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread 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); | ^~~~~~~~~~~~ s390x-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 `s390x-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 `s390x-linux-gnu-pkg-config --libs glib-2.0` s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread 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); | ^~~~~~~~~~~~ s390x-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 `s390x-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 `s390x-linux-gnu-pkg-config --libs glib-2.0` s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread 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); | ^~~~~~~~~~~~ s390x-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 `s390x-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 `s390x-linux-gnu-pkg-config --libs glib-2.0` s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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); | ^~~~~~~~~~~~ s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genomewise9.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genome_evidence.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ est_evidence.c s390x-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 `s390x-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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); | ^~~~~~~~~~~~ s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ sywise20.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ syexonmodel.c s390x-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 `s390x-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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); | ^~~~~~~~~~~~ s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ pseudowise7.c s390x-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 `s390x-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 `s390x-linux-gnu-pkg-config --libs glib-2.0` s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ `s390x-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); | ^~~~~~~~~~~~ s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ localdba.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ `s390x-linux-gnu-pkg-config --cflags glib-2.0` localcishit.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ localcispara.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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 -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ motifmatrixdp.c s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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/s390x-linux-gnu/include/stdio.h:970, 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/s390x-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 ()); | ~~~~~~~~~~~~~~~~~ s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ pairwiseshortdna.c s390x-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 `s390x-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase -lm `s390x-linux-gnu-pkg-config --libs glib-2.0` -lpthread s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -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); | ^~~~~~~~~~~~ s390x-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -I/usr/include/glib-2.0 -I/usr/lib/s390x-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ `s390x-linux-gnu-pkg-config --cflags glib-2.0` hsp2aln_sw.c s390x-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 `s390x-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 `s390x-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 3.141592653-2.6-1.40.28 (TeX Live 2025/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./api.tex LaTeX2e <2025-11-01> L3 programming layer <2026-01-19> (/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 2025/01/22 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] 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 2025/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 2025/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, 298545 bytes). Transcript written on api.log. cd docs && pdflatex api.tex This is pdfTeX, Version 3.141592653-2.6-1.40.28 (TeX Live 2025/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./api.tex LaTeX2e <2025-11-01> L3 programming layer <2026-01-19> (/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 2025/01/22 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] [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, 313855 bytes). Transcript written on api.log. cd docs && pdflatex dynamite.tex This is pdfTeX, Version 3.141592653-2.6-1.40.28 (TeX Live 2025/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./dynamite.tex LaTeX2e <2025-11-01> L3 programming layer <2026-01-19> (/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 2025/01/22 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, 220909 bytes). Transcript written on dynamite.log. cd docs && pdflatex dynamite.tex This is pdfTeX, Version 3.141592653-2.6-1.40.28 (TeX Live 2025/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./dynamite.tex LaTeX2e <2025-11-01> L3 programming layer <2026-01-19> (/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 2025/01/22 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, 224495 bytes). Transcript written on dynamite.log. cd docs && pdflatex wise2.tex This is pdfTeX, Version 3.141592653-2.6-1.40.28 (TeX Live 2025/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./wise2.tex LaTeX2e <2025-11-01> L3 programming layer <2026-01-19> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2025/01/22 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, 210558 bytes). Transcript written on wise2.log. cd docs && pdflatex wise2.tex This is pdfTeX, Version 3.141592653-2.6-1.40.28 (TeX Live 2025/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./wise2.tex LaTeX2e <2025-11-01> L3 programming layer <2026-01-19> (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2025/01/22 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, 213051 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/s390x-linux-gnu dwz -mdebian/wise/usr/lib/debug/.dwz/s390x-linux-gnu/wise.debug -M/usr/lib/debug/.dwz/s390x-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 s390x-linux-gnu-objcopy --compress-debug-sections debian/wise/usr/lib/debug/.dwz/s390x-linux-gnu/wise.debug chmod 0644 -- debian/wise/usr/lib/debug/.dwz/s390x-linux-gnu/wise.debug dh_strip -a install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/7c s390x-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genewisedb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/7c/5f5223386c60892d2f71c3040d57ee9a4be976.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/7c/5f5223386c60892d2f71c3040d57ee9a4be976.debug s390x-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genewisedb s390x-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/7c/5f5223386c60892d2f71c3040d57ee9a4be976.debug debian/wise/usr/bin/genewisedb install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/89 s390x-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genewise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/89/1bba940fedaf2c59b16e1350eaf9d9de4a854e.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/89/1bba940fedaf2c59b16e1350eaf9d9de4a854e.debug s390x-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genewise s390x-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/89/1bba940fedaf2c59b16e1350eaf9d9de4a854e.debug debian/wise/usr/bin/genewise install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fc s390x-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/estwisedb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fc/ae478ca7d5621c53250ee7e21c8d598b7ff295.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fc/ae478ca7d5621c53250ee7e21c8d598b7ff295.debug s390x-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/estwisedb s390x-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fc/ae478ca7d5621c53250ee7e21c8d598b7ff295.debug debian/wise/usr/bin/estwisedb install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/16 s390x-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/estwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/16/21239353b17ecf18e21f91b28f412a058d4cb3.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/16/21239353b17ecf18e21f91b28f412a058d4cb3.debug s390x-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/estwise s390x-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/16/21239353b17ecf18e21f91b28f412a058d4cb3.debug debian/wise/usr/bin/estwise install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/58 s390x-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/scanwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/58/ce74708d24383d5e985692896bae204d2c569d.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/58/ce74708d24383d5e985692896bae204d2c569d.debug s390x-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/scanwise s390x-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/58/ce74708d24383d5e985692896bae204d2c569d.debug debian/wise/usr/bin/scanwise install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/da s390x-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/da/d518708c77dcac32518f6fe1d317ad9c93158c.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/da/d518708c77dcac32518f6fe1d317ad9c93158c.debug s390x-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/scanwise_server s390x-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/da/d518708c77dcac32518f6fe1d317ad9c93158c.debug debian/wise/usr/bin/scanwise_server install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/8b s390x-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/pswdb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/8b/caa077e1f6fcd84d1eb15780e9235f9e797c5f.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/8b/caa077e1f6fcd84d1eb15780e9235f9e797c5f.debug s390x-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/pswdb s390x-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/8b/caa077e1f6fcd84d1eb15780e9235f9e797c5f.debug debian/wise/usr/bin/pswdb install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/2f s390x-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/psw debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/2f/f220516eb55e538f830eef24a6a421d0a32ef7.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/2f/f220516eb55e538f830eef24a6a421d0a32ef7.debug s390x-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/psw s390x-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/2f/f220516eb55e538f830eef24a6a421d0a32ef7.debug debian/wise/usr/bin/psw install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/13 s390x-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/promoterwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/13/681cc9f3880806dd6ef59dfad63846c30cf102.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/13/681cc9f3880806dd6ef59dfad63846c30cf102.debug s390x-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/promoterwise s390x-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/13/681cc9f3880806dd6ef59dfad63846c30cf102.debug debian/wise/usr/bin/promoterwise install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/59 s390x-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genomewise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/59/c79614f705d060d1a7d4eb3ab9def246f97550.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/59/c79614f705d060d1a7d4eb3ab9def246f97550.debug s390x-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genomewise s390x-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/59/c79614f705d060d1a7d4eb3ab9def246f97550.debug debian/wise/usr/bin/genomewise install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/71 s390x-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/dba debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/71/e925f2f1d32fb9163b0a3a7005e41cffdc31dd.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/71/e925f2f1d32fb9163b0a3a7005e41cffdc31dd.debug s390x-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/dba s390x-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/71/e925f2f1d32fb9163b0a3a7005e41cffdc31dd.debug debian/wise/usr/bin/dba install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/84 s390x-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/dnal debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/84/173d932b04e35ba7febc2d7e2e8855f3547075.debug chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/84/173d932b04e35ba7febc2d7e2e8855f3547075.debug s390x-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/dnal s390x-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/84/173d932b04e35ba7febc2d7e2e8855f3547075.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/s390x-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 -cdebian/control -Pdebian/.debhelper/wise/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=wise-dbgsym -DDepends="wise (= \${binary:Version})" -DDescription="debug symbols for wise" -DBuild-Ids="13681cc9f3880806dd6ef59dfad63846c30cf102 1621239353b17ecf18e21f91b28f412a058d4cb3 2ff220516eb55e538f830eef24a6a421d0a32ef7 58ce74708d24383d5e985692896bae204d2c569d 59c79614f705d060d1a7d4eb3ab9def246f97550 71e925f2f1d32fb9163b0a3a7005e41cffdc31dd 7c5f5223386c60892d2f71c3040d57ee9a4be976 84173d932b04e35ba7febc2d7e2e8855f3547075 891bba940fedaf2c59b16e1350eaf9d9de4a854e 8bcaa077e1f6fcd84d1eb15780e9235f9e797c5f dad518708c77dcac32518f6fe1d317ad9c93158c fcae478ca7d5621c53250ee7e21c8d598b7ff295" -DSection=debug -UMulti-Arch -UReplaces -UBreaks chmod 0644 -- debian/.debhelper/wise/dbgsym-root/DEBIAN/control dpkg-gencontrol -pwise -ldebian/changelog -Tdebian/wise.substvars -cdebian/control -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_2.4.1-28_s390x.deb'. dpkg-deb --root-owner-group --build debian/.debhelper/wise/dbgsym-root .. dpkg-deb: building package 'wise-dbgsym' in '../wise-dbgsym_2.4.1-28_s390x.deb'. dpkg-genbuildinfo --build=any -O../wise_2.4.1-28_s390x.buildinfo dpkg-genchanges --build=any -O../wise_2.4.1-28_s390x.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 2026-02-22T17:18:32Z +------------------------------------------------------------------------------+ | Finished Timed Build Commands | +------------------------------------------------------------------------------+ rm -Rf /<>/ ------------------------------------- I: Finished running 'rm -Rf /<>/'. Finished processing commands. -------------------------------------------------------------------------------- Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ wise_2.4.1-28_s390x.changes: ---------------------------- Format: 1.8 Date: Thu, 19 Feb 2026 21:03:40 +0100 Source: wise Binary: wise wise-dbgsym Built-For-Profiles: cross nocheck Architecture: s390x Version: 2.4.1-28 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Santiago Vila Description: wise - comparison of biopolymers, like DNA and protein sequences Changes: wise (2.4.1-28) unstable; urgency=medium . * Team upload. * Fix clean target. * Fix old-fsf-address-in-copyright-file. * Drop "Rules-Requires-Root: no" (default). * Drop "Priority: optional" (default). * Update standards-version. * Simplify salsa-ci.yml. Checksums-Sha1: ba11fe781bfd95e78754a61069548d75ddbaf401 8434560 wise-dbgsym_2.4.1-28_s390x.deb f8e4463067eb59af817eab0232794f305e78eda8 10073 wise_2.4.1-28_s390x.buildinfo f5b27b58c3ac02e8475bf5023e73669561331628 1089308 wise_2.4.1-28_s390x.deb Checksums-Sha256: 1312044e5ddcda5c7d6fc14f82a99728253101a4511447757c15317c5b85e84d 8434560 wise-dbgsym_2.4.1-28_s390x.deb ad5da6dd6b2ca72634465404c1928a9f5e089c35f92da6b7e8c697c19d8d0bc1 10073 wise_2.4.1-28_s390x.buildinfo 2b86f3c57f012c9020d58662fc2a6113e95db11626913939c3337e8a320a72e2 1089308 wise_2.4.1-28_s390x.deb Files: 6a93593a511ca00ea60dec7b779cab4c 8434560 debug optional wise-dbgsym_2.4.1-28_s390x.deb fce4479a54abdef24b1b6c91454e6514 10073 science optional wise_2.4.1-28_s390x.buildinfo 76011137ec159e401fb2158fffb83937 1089308 science optional wise_2.4.1-28_s390x.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: wise Binary: wise wise-dbgsym Architecture: s390x Version: 2.4.1-28 Checksums-Md5: 6a93593a511ca00ea60dec7b779cab4c 8434560 wise-dbgsym_2.4.1-28_s390x.deb 76011137ec159e401fb2158fffb83937 1089308 wise_2.4.1-28_s390x.deb Checksums-Sha1: ba11fe781bfd95e78754a61069548d75ddbaf401 8434560 wise-dbgsym_2.4.1-28_s390x.deb f5b27b58c3ac02e8475bf5023e73669561331628 1089308 wise_2.4.1-28_s390x.deb Checksums-Sha256: 1312044e5ddcda5c7d6fc14f82a99728253101a4511447757c15317c5b85e84d 8434560 wise-dbgsym_2.4.1-28_s390x.deb 2b86f3c57f012c9020d58662fc2a6113e95db11626913939c3337e8a320a72e2 1089308 wise_2.4.1-28_s390x.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sun, 22 Feb 2026 17:18:31 +0000 Build-Path: /<> Installed-Build-Depends: autoconf (= 2.72-3.1), automake (= 1:1.18.1-3), autopoint (= 0.23.2-1), autotools-dev (= 20240727.1), base-files (= 14), base-passwd (= 3.6.8), bash (= 5.3-2), binutils (= 2.46-2), binutils-common (= 2.46-2), binutils-x86-64-linux-gnu (= 2.46-2), bsdextrautils (= 2.41.3-4), build-essential (= 12.12), bzip2 (= 1.0.8-6+b1), coreutils (= 9.7-3), cpp (= 4:15.2.0-5), cpp-15 (= 15.2.0-13), cpp-15-x86-64-linux-gnu (= 15.2.0-13), cpp-x86-64-linux-gnu (= 4:15.2.0-5), cross-exe-wrapper (= 0.2.6+b1), dash (= 0.5.12-12), debconf (= 1.5.92), debhelper (= 13.30), debianutils (= 5.23.2), dh-autoreconf (= 21+nmu1), dh-strip-nondeterminism (= 1.15.0-1), diffutils (= 1:3.12-1), docbook (= 4.5-11), docbook-to-man (= 1:2.0.0-50), dpkg (= 1.23.5), dpkg-dev (= 1.23.5), dwz (= 0.16-2), file (= 1:5.46-5+b1), findutils (= 4.10.0-3), flex (= 2.6.4-8.2+b5), fontconfig-config (= 2.17.1-5), fonts-lmodern (= 2.005-1), fonts-urw-base35 (= 20200910-8), g++ (= 4:15.2.0-5), g++-15 (= 15.2.0-13), g++-15-x86-64-linux-gnu (= 15.2.0-13), g++-x86-64-linux-gnu (= 4:15.2.0-5), gcc (= 4:15.2.0-5), gcc-15 (= 15.2.0-13), gcc-15-base (= 15.2.0-13), gcc-15-x86-64-linux-gnu (= 15.2.0-13), gcc-x86-64-linux-gnu (= 4:15.2.0-5), gettext (= 0.23.2-1), gettext-base (= 0.23.2-1), ghostscript (= 10.06.0~dfsg-3), girepository-tools (= 2.87.2-3), grep (= 3.12-1), groff-base (= 1.23.0-10), gzip (= 1.13-1), hevea (= 2.36-2+b5), hicolor-icon-theme (= 0.18-2), hostname (= 3.25), imagemagick (= 8:7.1.2.13+dfsg1-1), imagemagick-7-common (= 8:7.1.2.13+dfsg1-1), imagemagick-7.q16 (= 8:7.1.2.13+dfsg1-1), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-3), libarchive-zip-perl (= 1.68-1), libasan8 (= 15.2.0-13), libatomic1 (= 15.2.0-13), libattr1 (= 1:2.5.2-4), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1+b1), libavahi-client3 (= 0.8-18), libavahi-common-data (= 0.8-18), libavahi-common3 (= 0.8-18), libbinutils (= 2.46-2), libblkid-dev (= 2.41.3-4), libblkid1 (= 2.41.3-4), libbrotli1 (= 1.2.0-3), libbz2-1.0 (= 1.0.8-6+b1), libc-bin (= 2.42-13), libc-dev-bin (= 2.42-13), libc-gconv-modules-extra (= 2.42-13), libc6 (= 2.42-13), libc6-dev (= 2.42-13), libcairo2 (= 1.18.4-3), libcap-ng0 (= 0.9.1-1), libcap2 (= 1:2.75-10+b5), libcc1-0 (= 15.2.0-13), libcom-err2 (= 1.47.2-3+b8), libcrypt1 (= 1:4.5.1-1), libctf-nobfd0 (= 2.46-2), libctf0 (= 2.46-2), libcups2t64 (= 2.4.16-1), libdatrie1 (= 0.2.14-1), libdav1d7 (= 1.5.3-1+b1), libdb5.3t64 (= 5.3.28+dfsg2-11), libdbus-1-3 (= 1.16.2-3), libde265-0 (= 1.0.16-1+b1), libdebconfclient0 (= 0.282+b2), libdebhelper-perl (= 13.30), libdeflate0 (= 1.23-2+b1), libdpkg-perl (= 1.23.5), libelf1t64 (= 0.194-1), libexpat1 (= 2.7.4-1), libffi-dev (= 3.5.2-3+b1), libffi8 (= 3.5.2-3+b1), libfftw3-double3 (= 3.3.10-2+b2), libfile-homedir-perl (= 1.006-2), libfile-stripnondeterminism-perl (= 1.15.0-1), libfile-which-perl (= 1.27-2), libfl-dev (= 2.6.4-8.2+b5), libfl2 (= 2.6.4-8.2+b5), libfontconfig1 (= 2.17.1-5), libfontenc1 (= 1:1.1.8-1+b3), libfreetype6 (= 2.14.1+dfsg-2), libgcc-15-dev (= 15.2.0-13), libgcc-s1 (= 15.2.0-13), libgdbm-compat4t64 (= 1.26-1+b1), libgdbm6t64 (= 1.26-1+b1), libgio-2.0-dev (= 2.87.2-3), libgio-2.0-dev-bin (= 2.87.2-3), libgirepository-2.0-0 (= 2.87.2-3), libglib2.0-0t64 (= 2.87.2-3), libglib2.0-bin (= 2.87.2-3), libglib2.0-data (= 2.87.2-3), libglib2.0-dev (= 2.87.2-3), libglib2.0-dev-bin (= 2.87.2-3), libgmp10 (= 2:6.3.0+dfsg-5+b1), libgnutls30t64 (= 3.8.12-3), libgomp1 (= 15.2.0-13), libgprofng0 (= 2.46-2), libgraphite2-3 (= 1.3.14-11+b1), libgs-common (= 10.06.0~dfsg-3), libgs10 (= 10.06.0~dfsg-3), libgs10-common (= 10.06.0~dfsg-3), libgssapi-krb5-2 (= 1.22.1-2), libharfbuzz0b (= 12.3.2-2), libheif-plugin-dav1d (= 1.21.2-3), libheif-plugin-libde265 (= 1.21.2-3), libheif1 (= 1.21.2-3), libhogweed6t64 (= 3.10.2-1), libhwasan0 (= 15.2.0-13), libice6 (= 2:1.1.1-1+b1), libicu76 (= 76.1-4+b1), libidn12 (= 1.43-2+b1), libidn2-0 (= 2.3.8-4+b1), libijs-0.35 (= 0.35-16+b1), libisl23 (= 0.27-1+b1), libitm1 (= 15.2.0-13), libjansson4 (= 2.14-2+b4), libjbig0 (= 2.1-6.1+b3), libjbig2dec0 (= 0.20-1+b4), libjpeg62-turbo (= 1:2.1.5-4), libk5crypto3 (= 1.22.1-2), libkeyutils1 (= 1.6.3-6+b1), libkpathsea6 (= 2025.20250727.75242+ds-5), libkrb5-3 (= 1.22.1-2), libkrb5support0 (= 1.22.1-2), liblcms2-2 (= 2.17-1), liblerc4 (= 4.0.0+ds-5+b1), liblqr-1-0 (= 0.4.2-2.2), liblsan0 (= 15.2.0-13), libltdl7 (= 2.5.4-9), liblzma5 (= 5.8.2-2), libmagic-mgc (= 1:5.46-5+b1), libmagic1t64 (= 1:5.46-5+b1), libmagickcore-7.q16-10 (= 8:7.1.2.13+dfsg1-1), libmagickwand-7.q16-10 (= 8:7.1.2.13+dfsg1-1), libmd0 (= 1.1.0-2+b2), libmime-charset-perl (= 1.013.1-2), libmount-dev (= 2.41.3-4), libmount1 (= 2.41.3-4), libmpc3 (= 1.3.1-2+b1), libmpfi0 (= 1.5.4+ds-4+b1), libmpfr6 (= 4.2.2-2+b1), libncursesw6 (= 6.6+20251231-1), libnetpbm11t64 (= 2:11.13.03-1), libnettle8t64 (= 3.10.2-1), libopenjp2-7 (= 2.5.4-1), libosp5 (= 1.5.2-15.2), libp11-kit0 (= 0.26.2-2), libpam-modules (= 1.7.0-5+b1), libpam-modules-bin (= 1.7.0-5+b1), libpam-runtime (= 1.7.0-5), libpam0g (= 1.7.0-5+b1), libpaper-utils (= 2.2.5-0.3+b3), libpaper2 (= 2.2.5-0.3+b3), libpcre2-16-0 (= 10.46-1+b1), libpcre2-32-0 (= 10.46-1+b1), libpcre2-8-0 (= 10.46-1+b1), libpcre2-dev (= 10.46-1+b1), libpcre2-posix3 (= 10.46-1+b1), libperl5.40 (= 5.40.1-7), libpipeline1 (= 1.5.8-2), libpixman-1-0 (= 0.46.4-1+b1), libpkgconf7 (= 2.5.1-4), libpng16-16t64 (= 1.6.55-1), libpotrace0 (= 1.16-2+b3), libproc2-0 (= 2:4.0.4-9+b1), libptexenc1 (= 2025.20250727.75242+ds-5), libpython3-stdlib (= 3.13.9-3), libpython3.13-minimal (= 3.13.12-1), libpython3.13-stdlib (= 3.13.12-1), libquadmath0 (= 15.2.0-13), libraw23t64 (= 0.21.5b-1), libreadline8t64 (= 8.3-4), libseccomp2 (= 2.6.0-2+b1), libselinux-dev (= 3.9-4+b1), libselinux1 (= 3.9-4+b1), libsepol-dev (= 3.9-2), libsepol2 (= 3.9-2), libsframe3 (= 2.46-2), libsharpyuv0 (= 1.5.0-0.1+b1), libsm6 (= 2:1.2.6-1+b1), libsmartcols1 (= 2.41.3-4), libsombok3 (= 2.4.0-2+b3), libsqlite3-0 (= 3.46.1-9), libssl3t64 (= 3.5.5-1), libstdc++-15-dev (= 15.2.0-13), libstdc++6 (= 15.2.0-13), libsynctex2 (= 2025.20250727.75242+ds-5), libsysprof-capture-4-dev (= 50~beta-1), libsystemd0 (= 259.1-1), libtasn1-6 (= 4.21.0-2), libteckit0 (= 2.5.13+ds-1), libtexlua53-5 (= 2025.20250727.75242+ds-5), libtext-charwidth-perl (= 0.04-11+b5), libtext-wrapi18n-perl (= 0.06-10), libthai-data (= 0.1.30-1), libthai0 (= 0.1.30-1), libtiff6 (= 4.7.1-1), libtinfo6 (= 6.6+20251231-1), libtool (= 2.5.4-9), libtsan2 (= 15.2.0-13), libubsan1 (= 15.2.0-13), libuchardet0 (= 0.0.8-2+b1), libudev1 (= 259.1-1), libunicode-linebreak-perl (= 0.0.20190101-3), libunistring5 (= 1.3-2+b1), libuuid1 (= 2.41.3-4), libwebp7 (= 1.5.0-0.1+b1), libwebpdemux2 (= 1.5.0-0.1+b1), libwebpmux3 (= 1.5.0-0.1+b1), libx11-6 (= 2:1.8.12-1+b1), libx11-data (= 2:1.8.12-1), libxau6 (= 1:1.0.11-1+b1), libxaw7 (= 2:1.0.16-1+b1), libxcb-render0 (= 1.17.0-2+b2), libxcb-shm0 (= 1.17.0-2+b2), libxcb1 (= 1.17.0-2+b2), libxdmcp6 (= 1:1.1.5-2), libxext6 (= 2:1.3.4-1+b4), libxi6 (= 2:1.8.2-2), libxml2-16 (= 2.15.1+dfsg-2+b1), libxmu6 (= 2:1.1.3-4), libxpm4 (= 1:3.5.17-1+b4), libxrender1 (= 1:0.9.12-1+b1), libxt6t64 (= 1:1.2.1-1.3+b1), libyaml-tiny-perl (= 1.76-1), libzstd1 (= 1.5.7+dfsg-3+b1), libzzip-0-13t64 (= 0.13.78+dfsg.1-0.2), linux-libc-dev (= 6.18.12-1), lmodern (= 2.005-1), m4 (= 1.4.21-1), make (= 4.4.1-3), man-db (= 2.13.1-1), mawk (= 1.3.4.20260129-1), media-types (= 14.0.0), native-architecture (= 0.2.6), ncurses-base (= 6.6+20251231-1), ncurses-bin (= 6.6+20251231-1), netbase (= 6.5), netpbm (= 2:11.13.03-1), opensp (= 1.5.2-15.2), openssl-provider-legacy (= 3.5.5-1), patch (= 2.8-2), perl (= 5.40.1-7), perl-base (= 5.40.1-7), perl-modules-5.40 (= 5.40.1-7), pkgconf (= 2.5.1-4), pkgconf-bin (= 2.5.1-4), po-debconf (= 1.0.22), poppler-data (= 0.4.12-1), procps (= 2:4.0.4-9+b1), python3 (= 3.13.9-3), python3-minimal (= 3.13.9-3), python3-packaging (= 25.0-2), python3.13 (= 3.13.12-1), python3.13-minimal (= 3.13.12-1), qemu-user (= 1:10.2.1+ds-1), readline-common (= 8.3-4), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.26), sgml-base (= 1.31+nmu1), sgml-data (= 2.0.11+nmu1), sysvinit-utils (= 3.15-6), t1utils (= 1.41-4), tar (= 1.35+dfsg-4), tex-common (= 6.20), texlive-base (= 2025.20260124-1), texlive-binaries (= 2025.20250727.75242+ds-5), texlive-extra-utils (= 2025.20260124-1), texlive-latex-base (= 2025.20260124-1), texlive-luatex (= 2025.20260124-1), texlive-plain-generic (= 2025.20260124-1), tzdata (= 2025c-3), ucf (= 3.0052), util-linux (= 2.41.3-4), uuid-dev (= 2.41.3-4), x11-common (= 1:7.7+26), xdg-utils (= 1.2.1-2), xfonts-encodings (= 1:1.0.4-2.2), xfonts-utils (= 1:7.7+7), xml-core (= 0.19), xz-utils (= 5.8.2-2), zlib1g (= 1:1.3.dfsg+really1.3.1-3), zlib1g-dev (= 1:1.3.dfsg+really1.3.1-3) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" SOURCE_DATE_EPOCH="1771531420" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ wise-dbgsym_2.4.1-28_s390x.deb ------------------------------ new Debian package, version 2.0. size 8434560 bytes: control archive=1132 bytes. 813 bytes, 12 lines control 1352 bytes, 13 lines md5sums Package: wise-dbgsym Source: wise Version: 2.4.1-28 Auto-Built-Package: debug-symbols Architecture: s390x Maintainer: Debian Med Packaging Team Installed-Size: 20899 Depends: wise (= 2.4.1-28) Section: debug Priority: optional Description: debug symbols for wise Build-Ids: 13681cc9f3880806dd6ef59dfad63846c30cf102 1621239353b17ecf18e21f91b28f412a058d4cb3 2ff220516eb55e538f830eef24a6a421d0a32ef7 58ce74708d24383d5e985692896bae204d2c569d 59c79614f705d060d1a7d4eb3ab9def246f97550 71e925f2f1d32fb9163b0a3a7005e41cffdc31dd 7c5f5223386c60892d2f71c3040d57ee9a4be976 84173d932b04e35ba7febc2d7e2e8855f3547075 891bba940fedaf2c59b16e1350eaf9d9de4a854e 8bcaa077e1f6fcd84d1eb15780e9235f9e797c5f 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root/root 0 2026-02-19 20:03 ./usr/share/doc/wise-dbgsym -> wise wise_2.4.1-28_s390x.deb ----------------------- new Debian package, version 2.0. size 1089308 bytes: control archive=1968 bytes. 1724 bytes, 33 lines control 1742 bytes, 29 lines md5sums Package: wise Version: 2.4.1-28 Architecture: s390x Maintainer: Debian Med Packaging Team Installed-Size: 11536 Depends: libc6 (>= 2.38), libglib2.0-0t64 (>= 2.12.0), wise-data (= 2.4.1-28) Suggests: wise-doc (= 2.4.1-28) 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 2026-02-19 20:03 ./ drwxr-xr-x root/root 0 2026-02-19 20:03 ./usr/ drwxr-xr-x root/root 0 2026-02-19 20:03 ./usr/bin/ -rwxr-xr-x root/root 366896 2026-02-19 20:03 ./usr/bin/dba -rwxr-xr-x root/root 243944 2026-02-19 20:03 ./usr/bin/dnal -rwxr-xr-x root/root 2208040 2026-02-19 20:03 ./usr/bin/estwise -rwxr-xr-x root/root 2212232 2026-02-19 20:03 ./usr/bin/estwisedb -rwxr-xr-x root/root 2212232 2026-02-19 20:03 ./usr/bin/genewise -rwxr-xr-x root/root 2216400 2026-02-19 20:03 ./usr/bin/genewisedb -rwxr-xr-x root/root 407744 2026-02-19 20:03 ./usr/bin/genomewise -rwxr-xr-x root/root 436456 2026-02-19 20:03 ./usr/bin/promoterwise -rwxr-xr-x root/root 358632 2026-02-19 20:03 ./usr/bin/psw -rwxr-xr-x root/root 366904 2026-02-19 20:03 ./usr/bin/pswdb -rwxr-xr-x root/root 526568 2026-02-19 20:03 ./usr/bin/scanwise -rwxr-xr-x root/root 215256 2026-02-19 20:03 ./usr/bin/scanwise_server drwxr-xr-x root/root 0 2026-02-19 20:03 ./usr/share/ drwxr-xr-x root/root 0 2026-02-19 20:03 ./usr/share/doc/ drwxr-xr-x root/root 0 2026-02-19 20:03 ./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 2026-02-19 20:03 ./usr/share/doc/wise/README.Debian -rw-r--r-- root/root 1572 2026-02-19 20:03 ./usr/share/doc/wise/changelog.Debian.gz -rw-r--r-- root/root 4228 2026-02-19 20:03 ./usr/share/doc/wise/copyright -rw-r--r-- root/root 312 2026-02-19 20:03 ./usr/share/doc/wise/run-unit-test drwxr-xr-x root/root 0 2026-02-19 20:03 ./usr/share/man/ drwxr-xr-x root/root 0 2026-02-19 20:03 ./usr/share/man/man1/ -rw-r--r-- root/root 846 2026-02-19 20:03 ./usr/share/man/man1/dba.1.gz -rw-r--r-- root/root 557 2026-02-19 20:03 ./usr/share/man/man1/dnal.1.gz -rw-r--r-- root/root 595 2026-02-19 20:03 ./usr/share/man/man1/estwise.1.gz -rw-r--r-- root/root 594 2026-02-19 20:03 ./usr/share/man/man1/estwisedb.1.gz -rw-r--r-- root/root 594 2026-02-19 20:03 ./usr/share/man/man1/genewise.1.gz -rw-r--r-- root/root 595 2026-02-19 20:03 ./usr/share/man/man1/genewisedb.1.gz -rw-r--r-- root/root 605 2026-02-19 20:03 ./usr/share/man/man1/genomewise.1.gz -rw-r--r-- root/root 592 2026-02-19 20:03 ./usr/share/man/man1/promoterwise.1.gz -rw-r--r-- root/root 685 2026-02-19 20:03 ./usr/share/man/man1/psw.1.gz -rw-r--r-- root/root 585 2026-02-19 20:03 ./usr/share/man/man1/pswdb.1.gz -rw-r--r-- root/root 601 2026-02-19 20:03 ./usr/share/man/man1/scanwise.1.gz -rw-r--r-- root/root 584 2026-02-19 20:03 ./usr/share/man/man1/scanwise_server.1.gz lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:amd64 Filtered Build-Depends: lintian:amd64 dpkg-deb: warning: root directory /<>/sbuild-build-depends-lintian-dummy has unusual owner or group 1000:119 dpkg-deb: hint: you might need to pass --root-owner-group, see for further details dpkg-deb: warning: ignoring 1 warning about the control file(s) 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 [1387 B] Get:5 copy:/<>/apt_archive ./ Packages [1466 B] Fetched 3468 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: appstream ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libappstream5 libapt-pkg-perl libassuan9 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-inspector-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libcurl3t64-gnutls 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-find-rule-perl libfile-libmagic-perl libfile-listing-perl libfile-sharedir-perl libfont-ttf-perl libfyaml0 libgcrypt20 libgpg-error0 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 libio-string-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl libksba8 libldap2 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 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnpth0t64 libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libpsl5t64 libregexp-wildcards-perl librole-tiny-perl librtmp1 libsasl2-2 libsasl2-modules-db libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libssh2-1t64 libstemmer0d 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-glob-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 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxmlb2 libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop openssl patchutils perl-openssl-defaults plzip shared-mime-info unzip Suggested packages: apt-config-icons isoquery libxml-parser-perl rng-tools libdata-dump-perl libcrypt-ssleay-perl libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libbusiness-isbn-perl libmime-base32-perl libregexp-ipv6-perl libauthen-ntlm-perl binutils-multiarch libtext-template-perl zip Recommended packages: gnupg libcgi-fast-perl libgpg-error-l10n libhtml-format-perl libio-compress-brotli-perl libldap-common liblist-someutils-xs-perl libfreezethaw-perl libmath-base85-perl libsocket6-perl libpackage-stash-xs-perl publicsuffix libsasl2-modules libxstring-perl libdata-dump-perl libhttp-daemon-perl libmailtools-perl libxml-sax-expat-perl The following NEW packages will be installed: appstream ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libappstream5 libapt-pkg-perl libassuan9 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-inspector-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libcurl3t64-gnutls 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-find-rule-perl libfile-libmagic-perl libfile-listing-perl libfile-sharedir-perl libfont-ttf-perl libfyaml0 libgcrypt20 libgpg-error0 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 libio-string-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl libksba8 libldap2 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 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnpth0t64 libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libpsl5t64 libregexp-wildcards-perl librole-tiny-perl librtmp1 libsasl2-2 libsasl2-modules-db libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libssh2-1t64 libstemmer0d 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-glob-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 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxmlb2 libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop openssl patchutils perl-openssl-defaults plzip sbuild-build-depends-lintian-dummy:s390x shared-mime-info unzip 0 upgraded, 153 newly installed, 0 to remove and 0 not upgraded. Need to get 17.4 MB of archives. After this operation, 72.7 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [848 B] Get:2 http://localhost:3142/debian unstable/main amd64 openssl amd64 3.5.5-1 [1500 kB] Get:3 http://localhost:3142/debian unstable/main amd64 ca-certificates all 20250419 [162 kB] Get:4 http://localhost:3142/debian unstable/main amd64 shared-mime-info amd64 2.4-5+b3 [758 kB] Get:5 http://localhost:3142/debian unstable/main amd64 libnghttp3-9 amd64 1.12.0-1 [68.4 kB] Get:6 http://localhost:3142/debian unstable/main amd64 libngtcp2-16 amd64 1.16.0-1 [136 kB] Get:7 http://localhost:3142/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-10 [19.8 kB] Get:8 http://localhost:3142/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-10 [57.8 kB] Get:9 http://localhost:3142/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1+b1 [195 kB] Get:10 http://localhost:3142/debian unstable/main amd64 libnghttp2-14 amd64 1.68.0-1 [79.8 kB] Get:11 http://localhost:3142/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.16.0-1 [25.2 kB] Get:12 http://localhost:3142/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b2 [59.8 kB] Get:13 http://localhost:3142/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3+b1 [60.7 kB] Get:14 http://localhost:3142/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1+b1 [245 kB] Get:15 http://localhost:3142/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.19.0~rc2-1 [407 kB] Get:16 http://localhost:3142/debian unstable/main amd64 libfyaml0 amd64 0.9.4-1 [312 kB] Get:17 http://localhost:3142/debian unstable/main amd64 libstemmer0d amd64 3.0.1-1+b1 [133 kB] Get:18 http://localhost:3142/debian unstable/main amd64 libxmlb2 amd64 0.3.24-2 [63.7 kB] Get:19 http://localhost:3142/debian unstable/main amd64 libappstream5 amd64 1.1.2-1 [227 kB] Get:20 http://localhost:3142/debian unstable/main amd64 appstream amd64 1.1.2-1 [566 kB] Get:21 http://localhost:3142/debian unstable/main amd64 diffstat amd64 1.68-1 [35.2 kB] Get:22 http://localhost:3142/debian unstable/main amd64 libgpg-error0 amd64 1.58-2 [89.7 kB] Get:23 http://localhost:3142/debian unstable/main amd64 libassuan9 amd64 3.0.2-2+b1 [62.1 kB] Get:24 http://localhost:3142/debian unstable/main amd64 libgcrypt20 amd64 1.11.2-3+b1 [871 kB] Get:25 http://localhost:3142/debian unstable/main amd64 gpgconf amd64 2.4.8-5 [129 kB] Get:26 http://localhost:3142/debian unstable/main amd64 libksba8 amd64 1.6.7-2+b2 [136 kB] Get:27 http://localhost:3142/debian unstable/main amd64 libnpth0t64 amd64 1.8-3+b1 [23.6 kB] Get:28 http://localhost:3142/debian unstable/main amd64 gpg amd64 2.4.8-5 [639 kB] Get:29 http://localhost:3142/debian unstable/main amd64 iso-codes all 4.20.1-1 [3319 kB] Get:30 http://localhost:3142/debian unstable/main amd64 libaliased-perl all 0.34-3 [13.5 kB] Get:31 http://localhost:3142/debian unstable/main amd64 libapt-pkg-perl amd64 0.1.43 [68.4 kB] Get:32 http://localhost:3142/debian unstable/main amd64 libb-hooks-op-check-perl amd64 0.22-3+b3 [10.6 kB] Get:33 http://localhost:3142/debian unstable/main amd64 libdynaloader-functions-perl all 0.004-2 [12.2 kB] Get:34 http://localhost:3142/debian unstable/main amd64 libdevel-callchecker-perl amd64 0.009-3 [15.3 kB] Get:35 http://localhost:3142/debian unstable/main amd64 libparams-classify-perl amd64 0.015-2+b5 [22.5 kB] Get:36 http://localhost:3142/debian unstable/main amd64 libmodule-runtime-perl all 0.018-1 [17.8 kB] Get:37 http://localhost:3142/debian unstable/main amd64 libtry-tiny-perl all 0.32-1 [22.9 kB] Get:38 http://localhost:3142/debian unstable/main amd64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get:39 http://localhost:3142/debian unstable/main amd64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get:40 http://localhost:3142/debian unstable/main amd64 libvariable-magic-perl amd64 0.64-1+b1 [44.9 kB] Get:41 http://localhost:3142/debian unstable/main amd64 libb-hooks-endofscope-perl all 0.28-2 [17.6 kB] Get:42 http://localhost:3142/debian unstable/main amd64 libberkeleydb-perl amd64 0.66-2 [122 kB] Get:43 http://localhost:3142/debian unstable/main amd64 libcapture-tiny-perl all 0.50-1 [24.6 kB] Get:44 http://localhost:3142/debian unstable/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get:45 http://localhost:3142/debian unstable/main amd64 liburi-perl all 5.34-2 [111 kB] Get:46 http://localhost:3142/debian unstable/main amd64 libhtml-parser-perl amd64 3.83-1+b3 [99.7 kB] Get:47 http://localhost:3142/debian unstable/main amd64 libcgi-pm-perl all 4.71-1 [217 kB] Get:48 http://localhost:3142/debian unstable/main amd64 libclass-data-inheritable-perl all 0.10-1 [8632 B] Get:49 http://localhost:3142/debian unstable/main amd64 libclass-inspector-perl all 1.36-3 [17.5 kB] Get:50 http://localhost:3142/debian unstable/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get:51 http://localhost:3142/debian unstable/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b5 [36.1 kB] Get:52 http://localhost:3142/debian unstable/main amd64 libclone-perl amd64 0.47-1+b2 [13.9 kB] Get:53 http://localhost:3142/debian unstable/main amd64 libconfig-tiny-perl all 2.30-1 [18.9 kB] Get:54 http://localhost:3142/debian unstable/main amd64 libparams-util-perl amd64 1.102-3+b1 [24.4 kB] Get:55 http://localhost:3142/debian unstable/main amd64 libsub-install-perl all 0.929-1 [10.5 kB] Get:56 http://localhost:3142/debian unstable/main amd64 libdata-optlist-perl all 0.114-1 [10.6 kB] Get:57 http://localhost:3142/debian unstable/main amd64 libsub-exporter-perl all 0.990-1 [50.6 kB] Get:58 http://localhost:3142/debian unstable/main amd64 libconst-fast-perl all 0.014-2 [8792 B] Get:59 http://localhost:3142/debian unstable/main amd64 libcpanel-json-xs-perl amd64 4.40-1 [132 kB] Get:60 http://localhost:3142/debian unstable/main amd64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get:61 http://localhost:3142/debian unstable/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] Get:62 http://localhost:3142/debian unstable/main amd64 libiterator-perl all 0.03+ds1-2 [18.8 kB] Get:63 http://localhost:3142/debian unstable/main amd64 libiterator-util-perl all 0.02+ds1-2 [14.0 kB] Get:64 http://localhost:3142/debian unstable/main amd64 libdata-dpath-perl all 0.60-1 [41.8 kB] Get:65 http://localhost:3142/debian unstable/main amd64 libdata-messagepack-perl amd64 1.02-3 [32.6 kB] Get:66 http://localhost:3142/debian unstable/main amd64 libnet-domain-tld-perl all 1.75-4 [31.5 kB] Get:67 http://localhost:3142/debian unstable/main amd64 libdata-validate-domain-perl all 0.15-1 [11.9 kB] Get:68 http://localhost:3142/debian unstable/main amd64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB] Get:69 http://localhost:3142/debian unstable/main amd64 libnet-netmask-perl all 2.0003-1 [28.5 kB] Get:70 http://localhost:3142/debian unstable/main amd64 libnetaddr-ip-perl amd64 4.079+dfsg-2+b5 [98.1 kB] Get:71 http://localhost:3142/debian unstable/main amd64 libdata-validate-ip-perl all 0.31-1 [20.6 kB] Get:72 http://localhost:3142/debian unstable/main amd64 libdata-validate-uri-perl all 0.07-3 [11.0 kB] Get:73 http://localhost:3142/debian unstable/main amd64 libdevel-size-perl amd64 0.86-1 [24.1 kB] Get:74 http://localhost:3142/debian unstable/main amd64 libemail-address-xs-perl amd64 1.05-1+b4 [29.4 kB] Get:75 http://localhost:3142/debian unstable/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get:76 http://localhost:3142/debian unstable/main amd64 libipc-system-simple-perl all 1.30-2 [26.8 kB] Get:77 http://localhost:3142/debian unstable/main amd64 libfile-basedir-perl all 0.09-2 [15.1 kB] Get:78 http://localhost:3142/debian unstable/main amd64 libnumber-compare-perl all 0.03-3 [6332 B] Get:79 http://localhost:3142/debian unstable/main amd64 libtext-glob-perl all 0.11-3 [7676 B] Get:80 http://localhost:3142/debian unstable/main amd64 libfile-find-rule-perl all 0.35-1 [25.9 kB] Get:81 http://localhost:3142/debian unstable/main amd64 libfile-libmagic-perl amd64 1.23-2+b2 [31.1 kB] Get:82 http://localhost:3142/debian unstable/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:83 http://localhost:3142/debian unstable/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get:84 http://localhost:3142/debian unstable/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get:85 http://localhost:3142/debian unstable/main amd64 libfile-sharedir-perl all 1.118-3 [16.0 kB] Get:86 http://localhost:3142/debian unstable/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get:87 http://localhost:3142/debian unstable/main amd64 libfont-ttf-perl all 1.06-2 [318 kB] Get:88 http://localhost:3142/debian unstable/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get:89 http://localhost:3142/debian unstable/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get:90 http://localhost:3142/debian unstable/main amd64 libhttp-message-perl all 7.01-1 [80.0 kB] Get:91 http://localhost:3142/debian unstable/main amd64 libhtml-form-perl all 6.13-1 [32.6 kB] Get:92 http://localhost:3142/debian unstable/main amd64 libhtml-html5-entities-perl all 0.004-3 [21.0 kB] Get:93 http://localhost:3142/debian unstable/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get:94 http://localhost:3142/debian unstable/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get:95 http://localhost:3142/debian unstable/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get:96 http://localhost:3142/debian unstable/main amd64 perl-openssl-defaults amd64 7+b2 [6724 B] Get:97 http://localhost:3142/debian unstable/main amd64 libnet-ssleay-perl amd64 1.94-3+b1 [342 kB] Get:98 http://localhost:3142/debian unstable/main amd64 libio-socket-ssl-perl all 2.098-1 [229 kB] Get:99 http://localhost:3142/debian unstable/main amd64 libnet-http-perl all 6.24-1 [23.2 kB] Get:100 http://localhost:3142/debian unstable/main amd64 liblwp-protocol-https-perl all 6.14-1 [10.8 kB] Get:101 http://localhost:3142/debian unstable/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:102 http://localhost:3142/debian unstable/main amd64 libwww-perl all 6.81-1 [186 kB] Get:103 http://localhost:3142/debian unstable/main amd64 libhtml-tokeparser-simple-perl all 3.16-4 [39.1 kB] Get:104 http://localhost:3142/debian unstable/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get:105 http://localhost:3142/debian unstable/main amd64 libio-interactive-perl all 1.027-1 [11.8 kB] Get:106 http://localhost:3142/debian unstable/main amd64 libipc-run3-perl all 0.049-1 [31.5 kB] Get:107 http://localhost:3142/debian unstable/main amd64 libjson-maybexs-perl all 1.004008-1 [12.9 kB] Get:108 http://localhost:3142/debian unstable/main amd64 liblist-compare-perl all 0.55-2 [65.7 kB] Get:109 http://localhost:3142/debian unstable/main amd64 liblist-someutils-perl all 0.59-1 [37.1 kB] Get:110 http://localhost:3142/debian unstable/main amd64 liblist-utilsby-perl all 0.12-2 [15.5 kB] Get:111 http://localhost:3142/debian unstable/main amd64 liblz1 amd64 1.16~rc1-3 [39.8 kB] Get:112 http://localhost:3142/debian unstable/main amd64 liblzo2-2 amd64 2.10-3+b2 [57.4 kB] Get:113 http://localhost:3142/debian unstable/main amd64 libmarkdown2 amd64 2.2.7-2.1+b1 [36.5 kB] Get:114 http://localhost:3142/debian unstable/main amd64 libmldbm-perl all 2.05-4 [16.8 kB] Get:115 http://localhost:3142/debian unstable/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get:116 http://localhost:3142/debian unstable/main amd64 libsub-quote-perl all 2.006009-1 [21.3 kB] Get:117 http://localhost:3142/debian unstable/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get:118 http://localhost:3142/debian unstable/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:119 http://localhost:3142/debian unstable/main amd64 libmoox-aliases-perl all 0.001006-2 [7156 B] Get:120 http://localhost:3142/debian unstable/main amd64 libmouse-perl amd64 2.6.1-1 [143 kB] Get:121 http://localhost:3142/debian unstable/main amd64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get:122 http://localhost:3142/debian unstable/main amd64 libsub-identify-perl amd64 0.14-4 [11.0 kB] Get:123 http://localhost:3142/debian unstable/main amd64 libsub-name-perl amd64 0.28-1+b1 [12.5 kB] Get:124 http://localhost:3142/debian unstable/main amd64 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get:125 http://localhost:3142/debian unstable/main amd64 libpath-tiny-perl all 0.148-1 [56.7 kB] Get:126 http://localhost:3142/debian unstable/main amd64 libperlio-gzip-perl amd64 0.20-1+b4 [17.5 kB] Get:127 http://localhost:3142/debian unstable/main amd64 libperlio-utf8-strict-perl amd64 0.010-1+b3 [11.4 kB] Get:128 http://localhost:3142/debian unstable/main amd64 libproc-processtable-perl amd64 0.637-1+b1 [42.3 kB] Get:129 http://localhost:3142/debian unstable/main amd64 libregexp-wildcards-perl all 1.05-3 [14.1 kB] Get:130 http://localhost:3142/debian unstable/main amd64 libsereal-decoder-perl amd64 5.004+ds-1+b3 [100 kB] Get:131 http://localhost:3142/debian unstable/main amd64 libsereal-encoder-perl amd64 5.004+ds-1+b3 [104 kB] Get:132 http://localhost:3142/debian unstable/main amd64 libsort-versions-perl all 1.62-3 [8928 B] Get:133 http://localhost:3142/debian unstable/main amd64 libxs-parse-keyword-perl amd64 0.49-1 [66.1 kB] Get:134 http://localhost:3142/debian unstable/main amd64 libsyntax-keyword-try-perl amd64 0.31-1 [27.4 kB] Get:135 http://localhost:3142/debian unstable/main amd64 libterm-readkey-perl amd64 2.38-2+b4 [24.6 kB] Get:136 http://localhost:3142/debian unstable/main amd64 libtext-levenshteinxs-perl amd64 0.03-5+b4 [8720 B] Get:137 http://localhost:3142/debian unstable/main amd64 libtext-markdown-discount-perl amd64 0.18-1 [13.1 kB] Get:138 http://localhost:3142/debian unstable/main amd64 libtext-xslate-perl amd64 3.5.9-2+b2 [174 kB] Get:139 http://localhost:3142/debian unstable/main amd64 libtime-duration-perl all 1.21-2 [13.1 kB] Get:140 http://localhost:3142/debian unstable/main amd64 libtime-moment-perl amd64 0.46-1 [78.2 kB] Get:141 http://localhost:3142/debian unstable/main amd64 libunicode-utf8-perl amd64 0.63-1 [20.4 kB] Get:142 http://localhost:3142/debian unstable/main amd64 libwww-mechanize-perl all 2.20-1 [117 kB] Get:143 http://localhost:3142/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:144 http://localhost:3142/debian unstable/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get:145 http://localhost:3142/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-4 [53.4 kB] Get:146 http://localhost:3142/debian unstable/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-7 [314 kB] Get:147 http://localhost:3142/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-2+b1 [53.8 kB] Get:148 http://localhost:3142/debian unstable/main amd64 libyaml-libyaml-perl amd64 0.904.0+ds-1 [46.9 kB] Get:149 http://localhost:3142/debian unstable/main amd64 plzip amd64 1.13~rc1-3 [66.7 kB] Get:150 http://localhost:3142/debian unstable/main amd64 lzop amd64 1.04-2 [84.2 kB] Get:151 http://localhost:3142/debian unstable/main amd64 patchutils amd64 0.4.3-1 [79.1 kB] Get:152 http://localhost:3142/debian unstable/main amd64 unzip amd64 6.0-29 [173 kB] Get:153 http://localhost:3142/debian unstable/main amd64 lintian all 2.129.0 [1068 kB] Preconfiguring packages ... Fetched 17.4 MB in 0s (94.3 MB/s) Selecting previously unselected package openssl. (Reading database ... 49120 files and directories currently installed.) Preparing to unpack .../000-openssl_3.5.5-1_amd64.deb ... Unpacking openssl (3.5.5-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../001-ca-certificates_20250419_all.deb ... Unpacking ca-certificates (20250419) ... Selecting previously unselected package shared-mime-info. Preparing to unpack .../002-shared-mime-info_2.4-5+b3_amd64.deb ... Unpacking shared-mime-info (2.4-5+b3) ... Selecting previously unselected package libnghttp3-9:amd64. Preparing to unpack .../003-libnghttp3-9_1.12.0-1_amd64.deb ... Unpacking libnghttp3-9:amd64 (1.12.0-1) ... Selecting previously unselected package libngtcp2-16:amd64. Preparing to unpack .../004-libngtcp2-16_1.16.0-1_amd64.deb ... Unpacking libngtcp2-16:amd64 (1.16.0-1) ... Selecting previously unselected package libsasl2-modules-db:amd64. 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Setting up liblz1:amd64 (1.16~rc1-3) ... Setting up libberkeleydb-perl:amd64 (0.66-2) ... Setting up plzip (1.13~rc1-3) ... 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 libnpth0t64:amd64 (1.8-3+b1) ... Setting up libunicode-utf8-perl (0.63-1) ... Setting up libmouse-perl:amd64 (2.6.1-1) ... Setting up libgpg-error0:amd64 (1.58-2) ... Setting up libdata-messagepack-perl (1.02-3) ... Setting up libclass-inspector-perl (1.36-3) ... Setting up libdynaloader-functions-perl (0.004-2) ... Setting up libtext-glob-perl (0.11-3) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up liblist-compare-perl (0.55-2) ... Setting up libclone-perl:amd64 (0.47-1+b2) ... Setting up libyaml-0-2:amd64 (0.2.5-2+b1) ... Setting up libsub-identify-perl (0.14-4) ... Setting up libcpanel-json-xs-perl:amd64 (4.40-1) ... Setting up libhtml-tagset-perl (3.24-1) ... Setting up libxmlb2:amd64 (0.3.24-2) ... Setting up libdevel-size-perl (0.86-1) ... Setting up unzip (6.0-29) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libyaml-libyaml-perl (0.904.0+ds-1) ... Setting up libio-interactive-perl (1.027-1) ... Setting up libtry-tiny-perl (0.32-1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b2) ... Setting up libnghttp2-14:amd64 (1.68.0-1) ... Setting up perl-openssl-defaults:amd64 (7+b2) ... Setting up libmldbm-perl (2.05-4) ... Setting up libxml-namespacesupport-perl (1.12-2) ... Setting up libgcrypt20:amd64 (1.11.2-3+b1) ... Setting up liblzo2-2:amd64 (2.10-3+b2) ... Setting up libtime-moment-perl (0.46-1) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libconfig-tiny-perl (2.30-1) ... Setting up libsereal-encoder-perl (5.004+ds-1+b3) ... Setting up liblist-utilsby-perl (0.12-2) ... Setting up libnet-netmask-perl (2.0003-1) ... Setting up libsub-install-perl (0.929-1) ... Setting up libfyaml0:amd64 (0.9.4-1) ... Setting up libnumber-compare-perl (0.03-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-10) ... Setting up patchutils (0.4.3-1) ... Setting up libjson-maybexs-perl (1.004008-1) ... Setting up libxml-sax-base-perl (1.09-3) ... Setting up libio-string-perl (1.08-4) ... Setting up libnetaddr-ip-perl (4.079+dfsg-2+b5) ... Setting up libclass-data-inheritable-perl (0.10-1) ... Setting up libfile-find-rule-perl (0.35-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3+b1) ... Setting up libipc-system-simple-perl (1.30-2) ... Setting up libnet-domain-tld-perl (1.75-4) ... Setting up libperlio-utf8-strict-perl (0.010-1+b3) ... Setting up shared-mime-info (2.4-5+b3) ... Setting up diffstat (1.68-1) ... Setting up libvariable-magic-perl (0.64-1+b1) ... Setting up libio-html-perl (1.004-3) ... Setting up libb-hooks-op-check-perl:amd64 (0.22-3+b3) ... Setting up libfile-libmagic-perl (1.23-2+b2) ... Setting up libparams-util-perl (1.102-3+b1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-10) ... Setting up libtime-duration-perl (1.21-2) ... Setting up libtext-xslate-perl:amd64 (3.5.9-2+b2) ... Setting up libnghttp3-9:amd64 (1.12.0-1) ... Setting up libsub-exporter-progressive-perl (0.001013-3) ... Setting up libcapture-tiny-perl (0.50-1) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libsub-name-perl:amd64 (0.28-1+b1) ... Setting up libdata-validate-domain-perl (0.15-1) ... Setting up libproc-processtable-perl:amd64 (0.637-1+b1) ... Setting up libpath-tiny-perl (0.148-1) ... Setting up lzop (1.04-2) ... Setting up libassuan9:amd64 (3.0.2-2+b1) ... Setting up gpgconf (2.4.8-5) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libipc-run3-perl (0.049-1) ... Setting up libregexp-wildcards-perl (1.05-3) ... Setting up libfile-sharedir-perl (1.118-3) ... Setting up libaliased-perl (0.34-3) ... Setting up libngtcp2-16:amd64 (1.16.0-1) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006009-1) ... Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b5) ... Setting up libstemmer0d:amd64 (3.0.1-1+b1) ... Setting up libsort-versions-perl (1.62-3) ... Setting up libssh2-1t64:amd64 (1.11.1-1+b1) ... Setting up libterm-readkey-perl (2.38-2+b4) ... Setting up libfont-ttf-perl (1.06-2) ... Setting up openssl (3.5.5-1) ... Setting up libtext-levenshteinxs-perl (0.03-5+b4) ... Setting up libperlio-gzip-perl (0.20-1+b4) ... Setting up libhtml-html5-entities-perl (0.004-3) ... Setting up libsereal-decoder-perl (5.004+ds-1+b3) ... Setting up libmarkdown2:amd64 (2.2.7-2.1+b1) ... Setting up libldap2:amd64 (2.6.10+dfsg-1+b1) ... Setting up liburi-perl (5.34-2) ... Setting up iso-codes (4.20.1-1) ... Setting up libnet-ipv6addr-perl (1.02-1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.16.0-1) ... Setting up libdata-validate-ip-perl (0.31-1) ... Setting up libemail-address-xs-perl (1.05-1+b4) ... Setting up libnet-ssleay-perl:amd64 (1.94-3+b1) ... Setting up libksba8:amd64 (1.6.7-2+b2) ... 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 libcurl3t64-gnutls:amd64 (8.19.0~rc2-1) ... Setting up libnet-http-perl (6.24-1) ... Setting up libtext-markdown-discount-perl (0.18-1) ... Setting up libappstream5:amd64 (1.1.2-1) ... Setting up libexception-class-perl (1.45-1) ... Setting up libdevel-callchecker-perl:amd64 (0.009-3) ... Setting up libxml-sax-perl (1.02+dfsg-4) ... 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 ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 150 added, 0 removed; done. Setting up libdata-validate-uri-perl (0.07-3) ... Setting up libxs-parse-keyword-perl (0.49-1) ... Setting up appstream (1.1.2-1) ... ✔ Metadata cache was updated successfully. Setting up libdata-optlist-perl (0.114-1) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-7) ... 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... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libsyntax-keyword-try-perl (0.31-1) ... Setting up libhtml-parser-perl:amd64 (3.83-1+b3) ... Setting up libio-socket-ssl-perl (2.098-1) ... Setting up gpg (2.4.8-5) ... Setting up libsub-exporter-perl (0.990-1) ... Setting up libhttp-message-perl (7.01-1) ... Setting up libhtml-form-perl (6.13-1) ... 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+b5) ... Setting up libcgi-pm-perl (4.71-1) ... Setting up libmodule-runtime-perl (0.018-1) ... Setting up libconst-fast-perl (0.014-2) ... Setting up libdata-dpath-perl (0.60-1) ... 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 (0.28-2) ... Setting up libnamespace-clean-perl (0.27-2) ... Setting up liblwp-protocol-https-perl (6.14-1) ... Setting up libwww-perl (6.81-1) ... Setting up libhtml-tokeparser-simple-perl (3.16-4) ... Setting up libwww-mechanize-perl (2.20-1) ... Processing triggers for sgml-base (1.31+nmu1) ... Processing triggers for libc-bin (2.42-13) ... Setting up lintian (2.129.0) ... Processing triggers for man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up sbuild-build-depends-lintian-dummy:s390x (0.invalid.0) ... Processing triggers for ca-certificates (20250419) ... 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: n/a Build-Time: 145 Distribution: unstable Foreign Architectures: s390x Host Architecture: s390x Install-Time: 48 Job: wise_2.4.1-28 Lintian: pass Machine Architecture: amd64 Package: wise Package-Time: 203 Source-Version: 2.4.1-28 Space: n/a Status: successful Version: 2.4.1-28 -------------------------------------------------------------------------------- Finished at 2026-02-22T17:18:32Z Build needed 00:03:23, no disk space