sbuild (Debian sbuild) 0.85.0 (04 January 2023) on debian-ci-siliconvalley

+==============================================================================+
| wise 2.4.1-28 (riscv64)                      Sun, 22 Feb 2026 11:05:23 +0000 |
+==============================================================================+

Package: wise
Version: 2.4.1-28
Source Version: 2.4.1-28
Distribution: unstable
Machine Architecture: amd64
Host Architecture: riscv64
Build Architecture: amd64
Build Profiles: cross nocheck
Build Type: any

I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-2f8d7688-d555-42f3-b41f-3a315cce2421' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/wise-dksDJh/resolver-WqjzII' with '<<RESOLVERDIR>>'

+------------------------------------------------------------------------------+
| Update chroot                                                                |
+------------------------------------------------------------------------------+

Get:1 http://localhost:3142/debian unstable InRelease [187 kB]
Get:2 http://localhost:3142/debian unstable/contrib 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/non-free 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/contrib Sources T-2026-02-22-0802.29-F-2026-02-22-0802.29.pdiff [31 B]
Get:7 http://localhost:3142/debian unstable/main Sources T-2026-02-22-0802.29-F-2026-02-22-0202.11.pdiff [26.1 kB]
Get:8 http://localhost:3142/debian unstable/non-free Sources T-2026-02-22-0202.11-F-2026-02-22-0202.11.pdiff [2236 B]
Get:6 http://localhost:3142/debian unstable/contrib Sources T-2026-02-22-0802.29-F-2026-02-22-0802.29.pdiff [31 B]
Get:9 http://localhost:3142/debian unstable/main amd64 Packages T-2026-02-22-0802.29-F-2026-02-22-0202.11.pdiff [34.9 kB]
Get:7 http://localhost:3142/debian unstable/main Sources T-2026-02-22-0802.29-F-2026-02-22-0202.11.pdiff [26.1 kB]
Get:8 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-2026-02-22-0802.29-F-2026-02-22-0202.11.pdiff [34.9 kB]
Get:10 http://localhost:3142/debian unstable/main riscv64 Packages [9818 kB]
Fetched 10.3 MB in 3s (3861 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 (153 MB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/wise-dksDJh/wise-2.4.1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/wise-dksDJh' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| 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-riscv64:amd64, libc-dev:riscv64, libstdc++-dev:riscv64
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-riscv64:amd64, libc-dev:riscv64, libstdc++-dev:riscv64
dpkg-deb: warning: root directory /<<RESOLVERDIR>>/sbuild-build-depends-main-dummy has unusual owner or group 1000:119
dpkg-deb: hint: you might need to pass --root-owner-group, see <https://wiki.debian.org/Teams/Dpkg/RootlessBuilds> for further details
dpkg-deb: warning: ignoring 1 warning about the control file(s)
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [609 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [811 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [856 B]
Fetched 2276 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-riscv64-linux-gnu
  bsdextrautils cpp-15-riscv64-linux-gnu cpp-riscv64-linux-gnu
  cross-exe-wrapper:riscv64 crossbuild-essential-riscv64 debhelper
  dh-autoreconf dh-strip-nondeterminism docbook docbook-to-man dwz fakeroot
  file flex fontconfig-config fonts-lmodern fonts-urw-base35
  g++-15-riscv64-linux-gnu g++-riscv64-linux-gnu gcc-15-base:riscv64
  gcc-15-cross-base gcc-15-riscv64-linux-gnu gcc-15-riscv64-linux-gnu-base
  gcc-riscv64-linux-gnu gettext gettext-base ghostscript girepository-tools
  girepository-tools:riscv64 groff-base hevea hicolor-icon-theme imagemagick
  imagemagick-7-common imagemagick-7.q16 intltool-debian libarchive-zip-perl
  libasan8:riscv64 libasan8-riscv64-cross libatomic1:riscv64
  libatomic1-riscv64-cross libavahi-client3 libavahi-common-data
  libavahi-common3 libblkid-dev:riscv64 libblkid1:riscv64 libbrotli1
  libc-gconv-modules-extra:riscv64 libc6:riscv64 libc6-dev:riscv64
  libc6-dev-riscv64-cross libc6-riscv64-cross libcairo2 libcom-err2
  libcups2t64 libdatrie1 libdav1d7 libdbus-1-3 libde265-0 libdebhelper-perl
  libdeflate0 libelf1t64 libexpat1 libfakeroot libffi-dev:riscv64 libffi8
  libffi8:riscv64 libfftw3-double3 libfile-homedir-perl
  libfile-stripnondeterminism-perl libfile-which-perl libfl-dev:riscv64
  libfl2:riscv64 libfontconfig1 libfontenc1 libfreetype6 libgcc-15-dev:riscv64
  libgcc-15-dev-riscv64-cross libgcc-s1:riscv64 libgcc-s1-riscv64-cross
  libgio-2.0-dev:riscv64 libgio-2.0-dev-bin libgirepository-2.0-0
  libgirepository-2.0-0:riscv64 libglib2.0-0t64 libglib2.0-0t64:riscv64
  libglib2.0-bin libglib2.0-data libglib2.0-dev:riscv64 libglib2.0-dev-bin
  libgnutls30t64 libgomp1:riscv64 libgomp1-riscv64-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:riscv64 libitm1-riscv64-cross
  libjbig0 libjbig2dec0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkpathsea6
  libkrb5-3 libkrb5support0 liblcms2-2 liblerc4 liblqr-1-0 liblsan0:riscv64
  liblsan0-riscv64-cross libltdl7 libmagic-mgc libmagic1t64
  libmagickcore-7.q16-10 libmagickwand-7.q16-10 libmime-charset-perl
  libmount-dev:riscv64 libmount1:riscv64 libmpfi0 libncursesw6 libnetpbm11t64
  libopenjp2-7 libosp5 libp11-kit0 libpaper-utils libpaper2
  libpcre2-16-0:riscv64 libpcre2-32-0:riscv64 libpcre2-8-0:riscv64
  libpcre2-dev:riscv64 libpcre2-posix3:riscv64 libpipeline1 libpixman-1-0
  libpkgconf7 libpng16-16t64 libpotrace0 libproc2-0 libptexenc1
  libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libraw23t64
  libreadline8t64 libselinux-dev:riscv64 libselinux1:riscv64
  libsepol-dev:riscv64 libsepol2:riscv64 libsharpyuv0 libsm6 libsombok3
  libsqlite3-0 libstdc++-15-dev:riscv64 libstdc++-15-dev-riscv64-cross
  libstdc++6:riscv64 libstdc++6-riscv64-cross libsynctex2
  libsysprof-capture-4-dev:riscv64 libtasn1-6 libteckit0 libtexlua53-5
  libtext-charwidth-perl libtext-wrapi18n-perl libthai-data libthai0 libtiff6
  libtool libtsan2:riscv64 libtsan2-riscv64-cross libubsan1:riscv64
  libubsan1-riscv64-cross libuchardet0 libunicode-linebreak-perl libunistring5
  libuuid1:riscv64 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-riscv64-cross lmodern m4 man-db media-types
  native-architecture netbase netpbm opensp pkgconf:riscv64 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:riscv64 x11-common xdg-utils xfonts-encodings xfonts-utils
  xml-core zlib1g:riscv64 zlib1g-dev:riscv64
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-riscv64-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:riscv64
  libc-l10n:riscv64 locales:riscv64 libnss-nis:riscv64 libnss-nisplus:riscv64
  manpages-dev:riscv64 cups-common libfftw3-bin libfftw3-dev
  gir1.2-glib-2.0-dev:riscv64 libglib2.0-doc:riscv64 libgdk-pixbuf2.0-bin
  libxml2-utils low-memory-monitor low-memory-monitor:riscv64 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:riscv64 libmpfi-doc
  libstdc++-15-doc:riscv64 libtool-doc gfortran | fortran95-compiler
  uuid-runtime:riscv64 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:riscv64
  dbus libarchive-cpio-perl shared-mime-info xdg-user-dirs
  shared-mime-info:riscv64 xdg-user-dirs:riscv64 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-riscv64-linux-gnu
  bsdextrautils cpp-15-riscv64-linux-gnu cpp-riscv64-linux-gnu
  cross-exe-wrapper:riscv64 crossbuild-essential-riscv64 debhelper
  dh-autoreconf dh-strip-nondeterminism docbook docbook-to-man dwz fakeroot
  file flex fontconfig-config fonts-lmodern fonts-urw-base35
  g++-15-riscv64-linux-gnu g++-riscv64-linux-gnu gcc-15-base:riscv64
  gcc-15-cross-base gcc-15-riscv64-linux-gnu gcc-15-riscv64-linux-gnu-base
  gcc-riscv64-linux-gnu gettext gettext-base ghostscript girepository-tools
  girepository-tools:riscv64 groff-base hevea hicolor-icon-theme imagemagick
  imagemagick-7-common imagemagick-7.q16 intltool-debian libarchive-zip-perl
  libasan8:riscv64 libasan8-riscv64-cross libatomic1:riscv64
  libatomic1-riscv64-cross libavahi-client3 libavahi-common-data
  libavahi-common3 libblkid-dev:riscv64 libblkid1:riscv64 libbrotli1
  libc-gconv-modules-extra:riscv64 libc6:riscv64 libc6-dev:riscv64
  libc6-dev-riscv64-cross libc6-riscv64-cross libcairo2 libcom-err2
  libcups2t64 libdatrie1 libdav1d7 libdbus-1-3 libde265-0 libdebhelper-perl
  libdeflate0 libelf1t64 libexpat1 libfakeroot libffi-dev:riscv64 libffi8
  libffi8:riscv64 libfftw3-double3 libfile-homedir-perl
  libfile-stripnondeterminism-perl libfile-which-perl libfl-dev:riscv64
  libfl2:riscv64 libfontconfig1 libfontenc1 libfreetype6 libgcc-15-dev:riscv64
  libgcc-15-dev-riscv64-cross libgcc-s1:riscv64 libgcc-s1-riscv64-cross
  libgio-2.0-dev:riscv64 libgio-2.0-dev-bin libgirepository-2.0-0
  libgirepository-2.0-0:riscv64 libglib2.0-0t64 libglib2.0-0t64:riscv64
  libglib2.0-bin libglib2.0-data libglib2.0-dev:riscv64 libglib2.0-dev-bin
  libgnutls30t64 libgomp1:riscv64 libgomp1-riscv64-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:riscv64 libitm1-riscv64-cross
  libjbig0 libjbig2dec0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkpathsea6
  libkrb5-3 libkrb5support0 liblcms2-2 liblerc4 liblqr-1-0 liblsan0:riscv64
  liblsan0-riscv64-cross libltdl7 libmagic-mgc libmagic1t64
  libmagickcore-7.q16-10 libmagickwand-7.q16-10 libmime-charset-perl
  libmount-dev:riscv64 libmount1:riscv64 libmpfi0 libncursesw6 libnetpbm11t64
  libopenjp2-7 libosp5 libp11-kit0 libpaper-utils libpaper2
  libpcre2-16-0:riscv64 libpcre2-32-0:riscv64 libpcre2-8-0:riscv64
  libpcre2-dev:riscv64 libpcre2-posix3:riscv64 libpipeline1 libpixman-1-0
  libpkgconf7 libpng16-16t64 libpotrace0 libproc2-0 libptexenc1
  libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libraw23t64
  libreadline8t64 libselinux-dev:riscv64 libselinux1:riscv64
  libsepol-dev:riscv64 libsepol2:riscv64 libsharpyuv0 libsm6 libsombok3
  libsqlite3-0 libstdc++-15-dev:riscv64 libstdc++-15-dev-riscv64-cross
  libstdc++6:riscv64 libstdc++6-riscv64-cross libsynctex2
  libsysprof-capture-4-dev:riscv64 libtasn1-6 libteckit0 libtexlua53-5
  libtext-charwidth-perl libtext-wrapi18n-perl libthai-data libthai0 libtiff6
  libtool libtsan2:riscv64 libtsan2-riscv64-cross libubsan1:riscv64
  libubsan1-riscv64-cross libuchardet0 libunicode-linebreak-perl libunistring5
  libuuid1:riscv64 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-riscv64-cross lmodern m4 man-db media-types
  native-architecture netbase netpbm opensp pkgconf:riscv64 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:riscv64 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:riscv64
  x11-common xdg-utils xfonts-encodings xfonts-utils xml-core zlib1g:riscv64
  zlib1g-dev:riscv64
0 upgraded, 253 newly installed, 0 to remove and 0 not upgraded.
Need to get 457 MB of archives.
After this operation, 1890 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/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-riscv64-linux-gnu amd64 2.46-2 [1496 kB]
Get:81 http://localhost:3142/debian unstable/main amd64 gcc-15-riscv64-linux-gnu-base amd64 15.2.0-13cross1 [55.1 kB]
Get:82 http://localhost:3142/debian unstable/main amd64 cpp-15-riscv64-linux-gnu amd64 15.2.0-13cross1 [14.8 MB]
Get:83 http://localhost:3142/debian unstable/main amd64 cpp-riscv64-linux-gnu amd64 4:15.2.0-5 [5320 B]
Get:84 http://localhost:3142/debian unstable/main riscv64 gcc-15-base riscv64 15.2.0-13 [54.8 kB]
Get:85 http://localhost:3142/debian unstable/main riscv64 libgcc-s1 riscv64 15.2.0-13 [61.5 kB]
Get:86 http://localhost:3142/debian unstable/main riscv64 libc-gconv-modules-extra riscv64 2.42-13 [1125 kB]
Get:87 http://localhost:3142/debian unstable/main riscv64 libc6 riscv64 2.42-13 [1422 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 riscv64 cross-exe-wrapper riscv64 0.2.6+b1 [6836 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-riscv64-cross all 2.42-12cross1 [1189 kB]
Get:92 http://localhost:3142/debian unstable/main amd64 libgcc-s1-riscv64-cross all 15.2.0-13cross1 [61.5 kB]
Get:93 http://localhost:3142/debian unstable/main amd64 libgomp1-riscv64-cross all 15.2.0-13cross1 [129 kB]
Get:94 http://localhost:3142/debian unstable/main amd64 libitm1-riscv64-cross all 15.2.0-13cross1 [24.9 kB]
Get:95 http://localhost:3142/debian unstable/main amd64 libatomic1-riscv64-cross all 15.2.0-13cross1 [8236 B]
Get:96 http://localhost:3142/debian unstable/main amd64 libasan8-riscv64-cross all 15.2.0-13cross1 [2928 kB]
Get:97 http://localhost:3142/debian unstable/main amd64 liblsan0-riscv64-cross all 15.2.0-13cross1 [1325 kB]
Get:98 http://localhost:3142/debian unstable/main amd64 libtsan2-riscv64-cross all 15.2.0-13cross1 [2642 kB]
Get:99 http://localhost:3142/debian unstable/main amd64 libstdc++6-riscv64-cross all 15.2.0-13cross1 [666 kB]
Get:100 http://localhost:3142/debian unstable/main amd64 libubsan1-riscv64-cross all 15.2.0-13cross1 [1177 kB]
Get:101 http://localhost:3142/debian unstable/main amd64 libgcc-15-dev-riscv64-cross all 15.2.0-13cross1 [5656 kB]
Get:102 http://localhost:3142/debian unstable/main amd64 gcc-15-riscv64-linux-gnu amd64 15.2.0-13cross1 [28.8 MB]
Get:103 http://localhost:3142/debian unstable/main amd64 gcc-riscv64-linux-gnu amd64 4:15.2.0-5 [1444 B]
Get:104 http://localhost:3142/debian unstable/main amd64 linux-libc-dev-riscv64-cross all 6.18.12-1 [11.8 kB]
Get:105 http://localhost:3142/debian unstable/main amd64 libc6-dev-riscv64-cross all 2.42-12cross1 [3432 kB]
Get:106 http://localhost:3142/debian unstable/main amd64 libstdc++-15-dev-riscv64-cross all 15.2.0-13cross1 [6427 kB]
Get:107 http://localhost:3142/debian unstable/main amd64 g++-15-riscv64-linux-gnu amd64 15.2.0-13cross1 [15.9 MB]
Get:108 http://localhost:3142/debian unstable/main amd64 g++-riscv64-linux-gnu amd64 4:15.2.0-5 [1200 B]
Get:109 http://localhost:3142/debian unstable/main amd64 crossbuild-essential-riscv64 all 12.12 [3544 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 riscv64 libffi8 riscv64 3.5.2-3+b1 [22.3 kB]
Get:160 http://localhost:3142/debian unstable/main riscv64 libatomic1 riscv64 15.2.0-13 [8580 B]
Get:161 http://localhost:3142/debian unstable/main riscv64 libblkid1 riscv64 2.41.3-4 [194 kB]
Get:162 http://localhost:3142/debian unstable/main riscv64 libpcre2-8-0 riscv64 10.46-1+b1 [297 kB]
Get:163 http://localhost:3142/debian unstable/main riscv64 libselinux1 riscv64 3.9-4+b1 [89.1 kB]
Get:164 http://localhost:3142/debian unstable/main riscv64 libmount1 riscv64 2.41.3-4 [227 kB]
Get:165 http://localhost:3142/debian unstable/main riscv64 zlib1g riscv64 1:1.3.dfsg+really1.3.1-3 [85.7 kB]
Get:166 http://localhost:3142/debian unstable/main riscv64 libglib2.0-0t64 riscv64 2.87.2-3 [1556 kB]
Get:167 http://localhost:3142/debian unstable/main riscv64 libgirepository-2.0-0 riscv64 2.87.2-3 [148 kB]
Get:168 http://localhost:3142/debian unstable/main riscv64 girepository-tools riscv64 2.87.2-3 [150 kB]
Get:169 http://localhost:3142/debian unstable/main amd64 native-architecture all 0.2.6 [2264 B]
Get:170 http://localhost:3142/debian unstable/main amd64 libgirepository-2.0-0 amd64 2.87.2-3 [147 kB]
Get:171 http://localhost:3142/debian unstable/main amd64 girepository-tools amd64 2.87.2-3 [153 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 riscv64 libasan8 riscv64 15.2.0-13 [2937 kB]
Get:205 http://localhost:3142/debian unstable/main riscv64 libc6-dev riscv64 2.42-13 [3438 kB]
Get:206 http://localhost:3142/debian unstable/main riscv64 libuuid1 riscv64 2.41.3-4 [40.5 kB]
Get:207 http://localhost:3142/debian unstable/main riscv64 uuid-dev riscv64 2.41.3-4 [69.4 kB]
Get:208 http://localhost:3142/debian unstable/main riscv64 libblkid-dev riscv64 2.41.3-4 [542 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 riscv64 libffi-dev riscv64 3.5.2-3+b1 [88.4 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 riscv64 libfl2 riscv64 2.6.4-8.2+b5 [84.2 kB]
Get:214 http://localhost:3142/debian unstable/main riscv64 libfl-dev riscv64 2.6.4-8.2+b5 [85.7 kB]
Get:215 http://localhost:3142/debian unstable/main riscv64 libgomp1 riscv64 15.2.0-13 [131 kB]
Get:216 http://localhost:3142/debian unstable/main riscv64 libitm1 riscv64 15.2.0-13 [25.5 kB]
Get:217 http://localhost:3142/debian unstable/main riscv64 liblsan0 riscv64 15.2.0-13 [1326 kB]
Get:218 http://localhost:3142/debian unstable/main riscv64 libtsan2 riscv64 15.2.0-13 [2654 kB]
Get:219 http://localhost:3142/debian unstable/main riscv64 libstdc++6 riscv64 15.2.0-13 [715 kB]
Get:220 http://localhost:3142/debian unstable/main riscv64 libubsan1 riscv64 15.2.0-13 [1178 kB]
Get:221 http://localhost:3142/debian unstable/main riscv64 libgcc-15-dev riscv64 15.2.0-13 [5696 kB]
Get:222 http://localhost:3142/debian unstable/main riscv64 libsepol2 riscv64 3.9-2 [306 kB]
Get:223 http://localhost:3142/debian unstable/main riscv64 libsepol-dev riscv64 3.9-2 [1123 kB]
Get:224 http://localhost:3142/debian unstable/main riscv64 libpcre2-16-0 riscv64 10.46-1+b1 [276 kB]
Get:225 http://localhost:3142/debian unstable/main riscv64 libpcre2-32-0 riscv64 10.46-1+b1 [264 kB]
Get:226 http://localhost:3142/debian unstable/main riscv64 libpcre2-posix3 riscv64 10.46-1+b1 [63.9 kB]
Get:227 http://localhost:3142/debian unstable/main riscv64 libpcre2-dev riscv64 10.46-1+b1 [2138 kB]
Get:228 http://localhost:3142/debian unstable/main riscv64 libselinux-dev riscv64 3.9-4+b1 [332 kB]
Get:229 http://localhost:3142/debian unstable/main riscv64 libmount-dev riscv64 2.41.3-4 [32.1 kB]
Get:230 http://localhost:3142/debian unstable/main riscv64 libsysprof-capture-4-dev riscv64 50~beta-1 [120 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 riscv64 pkgconf riscv64 2.5.1-4 [33.6 kB]
Get:234 http://localhost:3142/debian unstable/main riscv64 zlib1g-dev riscv64 1:1.3.dfsg+really1.3.1-3 [996 kB]
Get:235 http://localhost:3142/debian unstable/main riscv64 libgio-2.0-dev riscv64 2.87.2-3 [4533 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 riscv64 libglib2.0-dev riscv64 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 riscv64 libstdc++-15-dev riscv64 15.2.0-13 [6162 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]
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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:riscv64 (15.2.0-13) ...
Setting up libmagickcore-7.q16-10:amd64 (8:7.1.2.13+dfsg1-1) ...
Setting up libc6:riscv64 (2.42-13) ...
Setting up libffi8:riscv64 (3.5.2-3+b1) ...
Setting up libasan8:riscv64 (15.2.0-13) ...
Setting up libc6-dev:riscv64 (2.42-13) ...
Setting up libtsan2:riscv64 (15.2.0-13) ...
Setting up libblkid1:riscv64 (2.41.3-4) ...
Setting up libstdc++6:riscv64 (15.2.0-13) ...
Setting up liblsan0:riscv64 (15.2.0-13) ...
Setting up libitm1:riscv64 (15.2.0-13) ...
Setting up libmagickwand-7.q16-10:amd64 (8:7.1.2.13+dfsg1-1) ...
Setting up zlib1g:riscv64 (1:1.3.dfsg+really1.3.1-3) ...
Setting up libgomp1:riscv64 (15.2.0-13) ...
Setting up libffi-dev:riscv64 (3.5.2-3+b1) ...
Setting up libpcre2-16-0:riscv64 (10.46-1+b1) ...
Setting up libpcre2-32-0:riscv64 (10.46-1+b1) ...
Setting up libatomic1:riscv64 (15.2.0-13) ...
Setting up libuuid1:riscv64 (2.41.3-4) ...
Setting up libsepol2:riscv64 (3.9-2) ...
Setting up libsepol-dev:riscv64 (3.9-2) ...
Setting up libfl2:riscv64 (2.6.4-8.2+b5) ...
Setting up libpcre2-8-0:riscv64 (10.46-1+b1) ...
Setting up cross-exe-wrapper:riscv64 (0.2.6+b1) ...
Setting up libubsan1:riscv64 (15.2.0-13) ...
Setting up zlib1g-dev:riscv64 (1:1.3.dfsg+really1.3.1-3) ...
Setting up libpcre2-posix3:riscv64 (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:riscv64 (15.2.0-13) ...
Setting up libpcre2-dev:riscv64 (10.46-1+b1) ...
Setting up libfl-dev:riscv64 (2.6.4-8.2+b5) ...
Setting up libselinux1:riscv64 (3.9-4+b1) ...
Setting up libstdc++-15-dev:riscv64 (15.2.0-13) ...
Setting up uuid-dev:riscv64 (2.41.3-4) ...
Setting up hevea (2.36-2+b5) ...
Setting up imagemagick (8:7.1.2.13+dfsg1-1) ...
Setting up libmount1:riscv64 (2.41.3-4) ...
Setting up libselinux-dev:riscv64 (3.9-4+b1) ...
Setting up libblkid-dev:riscv64 (2.41.3-4) ...
Setting up libglib2.0-0t64:riscv64 (2.87.2-3) ...
/var/lib/dpkg/info/libglib2.0-0t64:riscv64.postinst: 41: /usr/lib/riscv64-linux-gnu/glib-2.0/glib-compile-schemas: Exec format error
/var/lib/dpkg/info/libglib2.0-0t64:riscv64.postinst: 42: /usr/lib/riscv64-linux-gnu/glib-2.0/gio-querymodules: Exec format error
Setting up libmount-dev:riscv64 (2.41.3-4) ...
Setting up libgio-2.0-dev:riscv64 (2.87.2-3) ...
Setting up libgirepository-2.0-0:riscv64 (2.87.2-3) ...
Setting up girepository-tools:riscv64 (2.87.2-3) ...
Setting up libglib2.0-dev:riscv64 (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:riscv64 (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 (riscv64 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-riscv64-cross_15.2.0-13cross1 libstdc++6_15.2.0-13 libstdc++6-riscv64-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-riscv64-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-riscv64-linux-gnu_15.2.0-13cross1 cpp-15-x86-64-linux-gnu_15.2.0-13 cpp-riscv64-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-riscv64_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 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libatomic1-riscv64-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-riscv64-cross_2.42-12cross1 libc6-riscv64-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 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libstdc++-15-dev-riscv64-cross_15.2.0-13cross1 libstdc++6_15.2.0-13 libstdc++6-riscv64-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-riscv64-cross_15.2.0-13cross1 libubsan1_15.2.0-13 libubsan1-riscv64-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-riscv64-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 <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller@debian.org>, Charles Plessy <plessy@debian.org>, Andreas Tille <tille@debian.org>
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

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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 /<<PKGBUILDDIR>>
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.riscv64
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.oaLY97mphW/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-2f8d7688-d555-42f3-b41f-3a315cce2421
SCHROOT_UID=1000
SCHROOT_USER=crossqa
SHELL=/bin/sh
USER=crossqa
XDG_SESSION_CLASS=user

dpkg-buildpackage
-----------------

Command: dpkg-buildpackage --sanitize-env -ariscv64 -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 <sanvila@debian.org>
dpkg-architecture: warning: specified GNU system type riscv64-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 riscv64
 debian/rules clean
dh clean
   debian/rules override_dh_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
/usr/bin/make -C src clean
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
cd external ; /usr/bin/make clean
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/external'
(cd mott; make clean)
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/external/mott'
rm -f *.[oa]
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/external/mott'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/external'
if test -d dynlibsrc; then cd dynlibsrc ; rm -f *.[oa]; fi
if test -d models; then cd models ; rm -f *.[oa]; fi
if test -d base; then cd base ; rm -f *.[oa]; fi
if test -d socket; then cd socket ; rm -f *.[oa]; fi
if test -d dnaindex; then cd dnaindex ; rm -f *.[oa]; fi
if test -d network; then cd network ; rm -f *.[oa]; fi
if test -d dyc; then cd dyc ; rm -f *.[oa]; fi
if test -d HMMer2; then cd HMMer2 ; rm -f *.[oa]; fi
if test -d perl; then cd perl/Wise2/libs ; rm -f *.[oa]; fi
if test -x perl/Wise2/Makefile; then cd perl/Wise2/ ; /usr/bin/make clean; fi
if test -d oldbin; then rm -rf oldbin; fi
if test -d bin; then echo 'moving binaries to oldbin'; mv -f bin oldbin; fi
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
/usr/bin/make -C debian/manpages.d clean
make[2]: Entering directory '/<<PKGBUILDDIR>>/debian/manpages.d'
rm -f dba.1 dnal.1 estwise.1 estwisedb.1 genewise.1 genewisedb.1 genomewise.1 promoterwise.1 psw.1 pswdb.1 scanwise.1 scanwise_server.1
make[2]: Leaving directory '/<<PKGBUILDDIR>>/debian/manpages.d'
rm -f -r src/oldbin
for i in dba psw dnal genomewise pswdb scanwise estwise genewise sywise genewisedb promoterwise pseudowise estwisedb; do rm -f src/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 '/<<PKGBUILDDIR>>'
 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 '/<<PKGBUILDDIR>>'
# 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=riscv64-linux-gnu-pkg-config CXX=riscv64-linux-gnu-g\+\+ CC=riscv64-linux-gnu-gcc libwisebase.a
make[2]: Entering directory '/<<PKGBUILDDIR>>/src/base'
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wiseconfig.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wisestring.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wiseerror.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wisememman.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 *
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wiserandom.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wisetime.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wiseoverlay.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wisestreaminterface.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread commandline.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 '/<<PKGBUILDDIR>>/src/base'
dh_auto_build --sourcedirectory=src/dyc -- dyc
	cd src/dyc && make -j1 INSTALL="install --strip-program=true" PKG_CONFIG=riscv64-linux-gnu-pkg-config CXX=riscv64-linux-gnu-g\+\+ CC=riscv64-linux-gnu-gcc dyc
make[2]: Entering directory '/<<PKGBUILDDIR>>/src/dyc'
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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/riscv64-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 ());
      |                                   ~~~~~~~~~~~~~~~~~
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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);
      |                                               ~~~~~~~~~~~~~~~~^~
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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
riscv64-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 '/<<PKGBUILDDIR>>/src/dyc'
PATH="$PATH:/<<PKGBUILDDIR>>/src/dyc" \
dh_auto_build --sourcedirectory=src -- all
	cd src && make -j1 INSTALL="install --strip-program=true" PKG_CONFIG=riscv64-linux-gnu-pkg-config CXX=riscv64-linux-gnu-g\+\+ CC=riscv64-linux-gnu-gcc all
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
(cd base   ; make CC="riscv64-linux-gnu-gcc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  `riscv64-linux-gnu-pkg-config --cflags glib-2.0`" libwisebase.a )
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/base'
make[3]: 'libwisebase.a' is up to date.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/base'
(cd HMMer2 ; make CC="riscv64-linux-gnu-gcc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  `riscv64-linux-gnu-pkg-config --cflags glib-2.0`" libhmmer.a )
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/HMMer2'
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c alphabet.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c core_algorithms.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c debug.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c emit.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c emulation.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c histogram.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c hmmio.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c mathsupport.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c masks.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c misc.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c modelmakers.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c plan7.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c plan9.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c prior.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c tophits.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c trace.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c aligneval.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c alignio.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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/riscv64-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__
      |              ^~~~~~
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c dayhoff.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c file.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c getopt.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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)
      | ^~~~~~~
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c interleaved.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c iupac.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c msf.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c revcomp.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c selex.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c sqerror.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c sqio.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c sre_ctype.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c sre_math.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c sre_string.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c stack.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c translate.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -c types.c		
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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 '/<<PKGBUILDDIR>>/src/HMMer2'
(cd dynlibsrc ; make CC="riscv64-linux-gnu-gcc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  `riscv64-linux-gnu-pkg-config --cflags glib-2.0`" libdyna.a )
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/dynlibsrc'
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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);
      |                   ^~~~~~~~~~~~
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ dnamatrix.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ probability.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ alnrange.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ alnconvert.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ basematrix.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ shattermatrix.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ dpenvelope.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ dbsearchimpl.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ dprunimpl.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ complexsequence.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ complexevalset.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ complexconsensi.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ sequence.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ sequencestream.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ seqalign.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hitlist.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hsp.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hspstream.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ codon.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ compmat.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ codonmatrix.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ codonmapper.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ sequencedb.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hscore.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ seqlookup.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ arrayseqlookup.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ genericindexresult.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ linkedlist_lookpos.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ singlenumberspace.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ histogram.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ searchstatinterface.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ searchstatlookup.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ proteindb.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ protein.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ pairbase.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ pairbaseseq.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ genomicdb.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ randommodel.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ randomdb.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ genomic.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ cdna.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ cdnadb.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ dna.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ embl.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ gene.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ transcript.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ translation.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ btcanvas.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ asciibtcanvas.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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 '/<<PKGBUILDDIR>>/src/dynlibsrc'
(cd dynlibsrc ; make CC="riscv64-linux-gnu-gcc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  `riscv64-linux-gnu-pkg-config --cflags glib-2.0`" libdyna_glib.a )
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/dynlibsrc'
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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);
      |                           ^
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ intallocator.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ proteinstreamedindex.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ shadowseq.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hsphandler.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hspscaninterface.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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}
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hsplookupscan.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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 *
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hspscanruntime.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ hsptwohitscan.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ proteinindexcons.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ dnaindexcons.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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 '/<<PKGBUILDDIR>>/src/dynlibsrc'
(cd external ;  make CC="riscv64-linux-gnu-gcc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  `riscv64-linux-gnu-pkg-config --cflags glib-2.0`" all )
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/external'
(cd mott; make CC="riscv64-linux-gnu-gcc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread" all)
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/external/mott'
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -Wdate-time -D_FORTIFY_SOURCE=2  -c -o gaplib.o gaplib.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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 '/<<PKGBUILDDIR>>/src/external/mott'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/external'
(cd socket ; make CC="riscv64-linux-gnu-gcc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  `riscv64-linux-gnu-pkg-config --cflags glib-2.0`" libwisesocket.a )
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/socket'
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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);
      |         ^~~~~~~~~~~~~~~~~~~~~~~
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ functionclient.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ anonobj.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ transferinterface.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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 '/<<PKGBUILDDIR>>/src/socket'
(cd dnaindex ; make CC="riscv64-linux-gnu-gcc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  `riscv64-linux-gnu-pkg-config --cflags glib-2.0`" all )
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/dnaindex'
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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]);
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models kmer_index_interface.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models kmer_direct.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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}
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models kmer_count.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models kmer_glib_index.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models singleseqspace.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models dnamapping.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models largeseqreader.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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}
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_contig.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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 *
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models assembly.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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 '/<<PKGBUILDDIR>>/src/dnaindex'
(cd network ; make  CC="riscv64-linux-gnu-gcc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  `riscv64-linux-gnu-pkg-config --cflags glib-2.0`" all )
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/network'
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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);
      |                                                                                                       ^~~~~~~~~~~~
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/  -I../socket -I../dynlibsrc -I../dnaindex net_hspscan.c
riscv64-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 `riscv64-linux-gnu-pkg-config --libs glib-2.0` -lpthread 
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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 '/<<PKGBUILDDIR>>/src/network'
(cd models  ; make CC="riscv64-linux-gnu-gcc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  `riscv64-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 '/<<PKGBUILDDIR>>/src/models'
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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);
      |                                                                                                       ^~~~~~~~~~~~
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ dnaalign.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ seqaligndisplay.c
riscv64-linux-gnu-gcc -o dnal dnal.o dnaalign.o seqaligndisplay.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `riscv64-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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);
      |                                                                                                       ^~~~~~~~~~~~
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ proteinsw.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ sw_wrap.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ abc.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ pba.c
riscv64-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 `riscv64-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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);
      |                                                                                                          ^~~~~~~~~~~~
riscv64-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 `riscv64-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ dba.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ slimdba.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ bigdba.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ dbadisplay.c
riscv64-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 `riscv64-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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);
      |                                                                                                       ^~~~~~~~~~~~
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneparser21.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneparameter.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genestats.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genewisehsp.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneutil.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneoutput.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ threestatemodel.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genefrequency.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ splicesitemodeler.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genewise4.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genewise6.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genestretch6.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genewise21.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneloop21.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneloop6.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genephase6.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ gwlite.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ gwlitemodel.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ gwrap.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ matchsum.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estwrap.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genewisemodel.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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/riscv64-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/riscv64-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/riscv64-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);
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ cdparser.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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);
      |                    ^~~~~~~~~~~~~~~~
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estwise3.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estslim3.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estloop3.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estfrag3.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estslimloop.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ gwquickdb.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ threestatedb.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ pfamhmmer1db.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ pwmdna.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../HMMer2/ -DHMMER_INTERNAL -I../base/ -I../dynlibsrc/ wise2xhmmer2.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genewisemodeldb.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ seqhit.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ standardout.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ geneparser4.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ estquick3.c
riscv64-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 `riscv64-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 `riscv64-linux-gnu-pkg-config --libs glib-2.0`
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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);
      |                                                                                                       ^~~~~~~~~~~~
riscv64-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 `riscv64-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 `riscv64-linux-gnu-pkg-config --libs glib-2.0`
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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);
      |                                                                                                       ^~~~~~~~~~~~
riscv64-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 `riscv64-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 `riscv64-linux-gnu-pkg-config --libs glib-2.0`
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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);
      |                                                                                                       ^~~~~~~~~~~~
riscv64-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 `riscv64-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 `riscv64-linux-gnu-pkg-config --libs glib-2.0`
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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);
      |                                                                                                       ^~~~~~~~~~~~
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genomewise9.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ genome_evidence.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ est_evidence.c
riscv64-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 `riscv64-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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);
      |                                                                                                       ^~~~~~~~~~~~
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ sywise20.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ syexonmodel.c
riscv64-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 `riscv64-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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);
      |                                                                                                       ^~~~~~~~~~~~
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ pseudowise7.c
riscv64-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 `riscv64-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 `riscv64-linux-gnu-pkg-config --libs glib-2.0`
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ `riscv64-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);
      |                                                                                                       ^~~~~~~~~~~~
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ localdba.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ `riscv64-linux-gnu-pkg-config --cflags glib-2.0` localcishit.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ localcispara.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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<leni;i++)  {
      |                        ^
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ motifmatrixdp.c
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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/riscv64-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/riscv64-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 ());
      |                                   ~~~~~~~~~~~~~~~~~
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ pairwiseshortdna.c
riscv64-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 `riscv64-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm `riscv64-linux-gnu-pkg-config --libs glib-2.0` -lpthread
riscv64-linux-gnu-gcc  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-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);
      |                                                                                                       ^~~~~~~~~~~~
riscv64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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/riscv64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread -I../base/ -I../dynlibsrc/ `riscv64-linux-gnu-pkg-config --cflags glib-2.0` hsp2aln_sw.c
riscv64-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 `riscv64-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 `riscv64-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 '/<<PKGBUILDDIR>>/src/models'
make bin
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
mkdir bin
cp models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/promoterwise network/scanwise_server models/scanwise ./bin
./welcome.csh

Welcome to Wise2.4

The executable programs are in the ./bin directory

You must set your WISECONFIGDIR to the config directory
before using the programs

ie, type setenv WISECONFIGDIR /<<PKGBUILDDIR>>/src/../wisecfg/

to try an example, try cd example and then
../bin/genewise road.pep human.genomic

to build perl, type make perl and follow the instructions

to test the package, type make test
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
/usr/bin/make -C debian/manpages.d
make[2]: Entering directory '/<<PKGBUILDDIR>>/debian/manpages.d'
docbook-to-man dba.sgml > dba.1
docbook-to-man dnal.sgml > dnal.1
docbook-to-man estwise.sgml > estwise.1
docbook-to-man estwisedb.sgml > estwisedb.1
docbook-to-man genewise.sgml > genewise.1
docbook-to-man genewisedb.sgml > genewisedb.1
docbook-to-man genomewise.sgml > genomewise.1
docbook-to-man promoterwise.sgml > promoterwise.1
docbook-to-man psw.sgml > psw.1
docbook-to-man pswdb.sgml > pswdb.1
docbook-to-man scanwise.sgml > scanwise.1
docbook-to-man scanwise_server.sgml > scanwise_server.1
make[2]: Leaving directory '/<<PKGBUILDDIR>>/debian/manpages.d'
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]
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[]    \OT1/cmtt/m/n/10 print "You must give a file to revcom for a reverse to w
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[]\OT1/cmr/m/n/10 Build an en-tire pa-ram-e-ter set for ge-newise us-ing Wise2:
:GeneParameter21[]wrap

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text,dpri) 

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[]\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]
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[]\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]
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[]\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]
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[]\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.


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[]\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.


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[]\OT1/cmtt/m/n/10 Wise2[]Align[]strings[]ProteinSmithWaterman (one,two,comp,ga
p,ext,dpenv,dpri) 

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[]\OT1/cmtt/m/n/10 &Wise2::Align[]strings[]ProteinSmithWaterman (one,two,comp,g
ap,ext,dpenv,dpri) 
[96]
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[]\OT1/cmtt/m/n/10 Wise2[]Align[]Sequences[]ProteinSmithWaterman (one,two,comp,
gap,ext,dpenv,dpri) 

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[]\OT1/cmtt/m/n/10 &Wise2::Align[]Sequences[]ProteinSmithWaterman (one,two,comp
,gap,ext,dpenv,dpri) 

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[]\OT1/cmr/m/n/10 [OWNER] new AlnBlock struc-ture rep-re-sent-ing the align-men
t [AlnBlock
[97]
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[]\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]SmithWaterman (one,two,comp,gap,ext,
dpenv,dpri) 

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[]\OT1/cmtt/m/n/10 &Wise2::Align[]Proteins[]SmithWaterman (one,two,comp,gap,ext
,dpenv,dpri) 

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[]\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]ABC (one,two,comp,a,b,c,dpenv,dpri) 

[98]
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[]\OT1/cmtt/m/n/10 Wise2[]Align[]Sequences[]ProteinABC (one,two,comp,a,b,c,dpen
v,dpri) 

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[]\OT1/cmtt/m/n/10 &Wise2::Align[]Sequences[]ProteinABC (one,two,comp,a,b,c,dpe
nv,dpri) 

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\OT1/cmr/m/n/10 Align[]Sequences[]ProteinABC this func-tion is anal-o-gous to A
lign[]Sequences[]ProteinSmithWaterman

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[]\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinSW (querydb,targetdb,comp,gap,ex
t,bits[]cutoff,report[]level,die[]on[]error,dbsi) 

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[]\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinSW (querydb,targetdb,comp,gap,e
xt,bits[]cutoff,report[]level,die[]on[]error,dbsi) 
[99]
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[]\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b,c
,bits[]cutoff,report[]level,die[]on[]error,dbsi) 

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[]\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b,
c,bits[]cutoff,report[]level,die[]on[]error,dbsi) 
[100]
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[]\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) 

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[]\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]
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[]\OT1/cmr/m/n/10 reload[]generic Type [Three-State-Model * (*reload[]generic)(
ThreeStateDB * tdb,int

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[]\OT1/cmr/m/n/10 dataentry[]add Type [boolean (*dataen-try[]add)(ThreeStateDB 
* tdb,DataEntry

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[]\OT1/cmr/m/n/10 index[]generic Type [Three-State-Model * (*in-dex[]generic)(T
hreeStateDB *tdb,DataEntry
[102]
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[]\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) 

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[]\OT1/cmtt/m/n/10 Wise2[]force[]weighted[]local[]model (tsm,prob[]into[]model,
ratio[]start,ratio[]end) 

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[]\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::force[]weighted[]local[]model (tsm,
prob[]into[]model,ratio[]start,ratio[]end) 

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[]\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->force[]weighted[]local[]model(prob[]i
nto[]model,ratio[]start,ratio[]end) 

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[]\OT1/cmtt/m/n/10 Wise2[]ThreeStateModel[]from[]half[]bit[]Sequence (pro,mat,r
m,gap,ext) 
[106]
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[]\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::ThreeStateModel[]from[]half[]bit[]S
equence

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[]\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->ThreeStateModel[]from[]half[]bit[]Seq
uence(mat,rm,gap,ext) 

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[]\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
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LaTeX Warning: There were undefined references.


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 )
(see the transcript file for additional information) </tmp/texfonts/pk/ljfour/j
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dist/fonts/type1/public/amsfonts/cm/cmr17.pfb></usr/share/texlive/texmf-dist/fo
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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]
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[]    \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.



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[]\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
.


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\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]
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[]\OT1/cmtt/m/n/10 &Wise2::CodonMapper::sprinkle[]errors[]over[]CodonMapper (cm
,error) 
[37] [38] [39] [40] [41] [42] [43] [44] [45] [46]
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[]\OT1/cmtt/m/n/10 Wise2[]Genomic[]from[]Sequence[]Nheuristic (seq,length[]of[]
N) 
[47] [48] [49]
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[]\OT1/cmtt/m/n/10 Wise2[]new[]GenomicDB[]from[]single[]seq (gen,cses,score[]in
[]repeat[]coding) 

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[]\OT1/cmtt/m/n/10 &Wise2::new[]GenomicDB[]from[]single[]seq (gen,cses,score[]i
n[]repeat[]coding) 

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[]\OT1/cmtt/m/n/10 Wise2[]new[]GenomicDB (seqdb,cses,length[]of[]N,repeat[]in[]
cds[]score) 

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[]\OT1/cmtt/m/n/10 &Wise2::new[]GenomicDB (seqdb,cses,length[]of[]N,repeat[]in[
]cds[]score) 
[50] [51] [52]
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[]\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::read[]EMBL[]GenomicRegion[]file (file
name) 
[53]
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[]\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::show[]ace[]GenomicRegion (gr,seq[]nam
e,ofp) 

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[]\OT1/cmtt/m/n/10 Wise2[]show[]pretty[]GenomicRegion (gr,show[]supporting,ofp)
 

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[]\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::show[]pretty[]GenomicRegion (gr,show[
]supporting,ofp) 
[54] [55] [56]
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[]   \OT1/cmtt/m/n/10 b) cooperation with future versions of histogram.c would 
be possible.[] 
[57] [58] [59]
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[]\OT1/cmtt/m/n/10 Wise2[]ExtremeValueSetHistogram (h,mu,lambda,lowbound,highbo
und,wonka,ndegrees) 

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[]\OT1/cmtt/m/n/10 &Wise2::Histogram::set[]EVD (h,mu,lambda,lowbound,highbound,
wonka,ndegrees) 

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[]\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->set[]EVD(mu,lambda,lowbound,highbound
,wonka,ndegrees) 
[60] [61] [62]
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[]\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]
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[]\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]
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\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]
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[]\OT1/cmtt/m/n/10 Wise2[]make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap,
text,dpri) 

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[]\OT1/cmtt/m/n/10 &Wise2::make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap
,text,dpri) 
[90]
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[]\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) 

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[]\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]
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[]\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) 

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[]\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]
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[]\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) 

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[]\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]
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[]\OT1/cmtt/m/n/10 Wise2[]protein2genomic[]ascii[]display (alb,p,gen,ct,name,ma
in,ofp) 

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[]\OT1/cmtt/m/n/10 &Wise2::protein2genomic[]ascii[]display (alb,p,gen,ct,name,m
ain,ofp) 
[94]
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[]\OT1/cmtt/m/n/10 Wise2[]protcdna[]ascii[]display (alb,protsequence,protname,p
rotoff,cdna,ct,name,main,mult,ofp) 

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[]\OT1/cmtt/m/n/10 &Wise2::protcdna[]ascii[]display (alb,protsequence,protname,
protoff,cdna,ct,name,main,mult,ofp) 
[95]
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[]\OT1/cmr/m/n/10 transition[GENEFREQUENCY21[]TRANSITION[]LEN] Type [dou-ble : 
Scalar]
[96] [97]
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[]\OT1/cmtt/m/n/10 Wise2[]MatchSummarySet[]from[]AlnBlock[]estwise (alb,qname,o
ffset,target) 

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[]\OT1/cmtt/m/n/10 &Wise2::MatchSummarySet::MatchSummarySet[]from[]AlnBlock[]es
twise

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[]\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->MatchSummarySet[]from[]AlnBlock[]estw
ise(qname,offset,target) 
[98]
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[]\OT1/cmtt/m/n/10 Wise2[]MatchSummarySet[]from[]AlnBlock[]genewise (alb,qname,
protoff,target) 

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[]\OT1/cmtt/m/n/10 &Wise2::MatchSummarySet::MatchSummarySet[]from[]AlnBlock[]ge
newise

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[]\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->MatchSummarySet[]from[]AlnBlock[]gene
wise(qname,protoff,target) 
[99] [100]
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[]\OT1/cmtt/m/n/10 Wise2[]write[]pretty[]str[]align (alb,qname,query,tname,targ
et,name,main,ofp) 

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[]\OT1/cmtt/m/n/10 &Wise2::write[]pretty[]str[]align (alb,qname,query,tname,tar
get,name,main,ofp) 
[101]
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[]\OT1/cmtt/m/n/10 Wise2[]write[]pretty[]Protein[]align (alb,q,t,name,main,ofp)
 
[102]
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[]\OT1/cmtt/m/n/10 &Wise2::DnaSequenceHitList::read[]MSPcrunch[]DnaSequenceHitL
ist (ifp) 
[103]
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[]\OT1/cmtt/m/n/10 Wise2[]Align[]strings[]ProteinSmithWaterman (one,two,comp,ga
p,ext,dpenv,dpri) 

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[]\OT1/cmtt/m/n/10 &Wise2::Align[]strings[]ProteinSmithWaterman (one,two,comp,g
ap,ext,dpenv,dpri) 
[104]
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[]\OT1/cmtt/m/n/10 Wise2[]Align[]Sequences[]ProteinSmithWaterman (one,two,comp,
gap,ext,dpenv,dpri) 

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[]\OT1/cmtt/m/n/10 &Wise2::Align[]Sequences[]ProteinSmithWaterman (one,two,comp
,gap,ext,dpenv,dpri) 

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[]\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) 

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[]\OT1/cmtt/m/n/10 &Wise2::Align[]Proteins[]SmithWaterman (one,two,comp,gap,ext
,dpenv,dpri) 

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[]\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]ABC (one,two,comp,a,b,c,dpenv,dpri) 

[106]
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[]\OT1/cmtt/m/n/10 Wise2[]Align[]Sequences[]ProteinABC (one,two,comp,a,b,c,dpen
v,dpri) 

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[]\OT1/cmtt/m/n/10 &Wise2::Align[]Sequences[]ProteinABC (one,two,comp,a,b,c,dpe
nv,dpri) 

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\OT1/cmr/m/n/10 Align[]Sequences[]ProteinABC this func-tion is anal-o-gous to A
lign[]Sequences[]ProteinSmithWaterman

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[]\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinSW (querydb,targetdb,comp,gap,ex
t,bits[]cutoff,report[]level,die[]on[]error,dbsi) 

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[]\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinSW (querydb,targetdb,comp,gap,e
xt,bits[]cutoff,report[]level,die[]on[]error,dbsi) 
[107]
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[]\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b,c
,bits[]cutoff,report[]level,die[]on[]error,dbsi) 

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[]\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b,
c,bits[]cutoff,report[]level,die[]on[]error,dbsi) 
[108]
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[]\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) 

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[]\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]
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[]\OT1/cmr/m/n/10 reload[]generic Type [Three-State-Model * (*reload[]generic)(
ThreeStateDB * tdb,int

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[]\OT1/cmr/m/n/10 dataentry[]add Type [boolean (*dataen-try[]add)(ThreeStateDB 
* tdb,DataEntry

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[]\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]
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[]\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::force[]global[]model (tsm,prob[]int
o[]model) 

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[]\OT1/cmtt/m/n/10 Wise2[]force[]weighted[]local[]model (tsm,prob[]into[]model,
ratio[]start,ratio[]end) 

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[]\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::force[]weighted[]local[]model (tsm,
prob[]into[]model,ratio[]start,ratio[]end) 

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[]\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->force[]weighted[]local[]model(prob[]i
nto[]model,ratio[]start,ratio[]end) 

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[]\OT1/cmtt/m/n/10 Wise2[]ThreeStateModel[]from[]half[]bit[]Sequence (pro,mat,r
m,gap,ext) 
[114]
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[]\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::ThreeStateModel[]from[]half[]bit[]S
equence

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[]\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->ThreeStateModel[]from[]half[]bit[]Seq
uence(mat,rm,gap,ext) 

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[]\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::write[]HMMer[]1[]7[]ascii[]ThreeSta
teModel (tsm,ofp) 
[115] [116] (./api.aux)

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cd docs && pdflatex dynamite.tex
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entering extended mode
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[4] [5] [6]
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\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]
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[]  \OT1/cmtt/m/n/10 fprintf(ofp,"\npsw <options> seq1 seq2\nBoth sequences in 
fasta format\n"[] 

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[]   \OT1/cmtt/m/n/10 * -g for gap value (an int) - rely on commandline error p
rocessing[] 

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[]   \OT1/cmtt/m/n/10 * -e for ext value (an int) - rely on commandline error p
rocessing[] 
[11]
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[]  \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]
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[]   \OT1/cmtt/m/n/10 * or WISEPERSONALDIR if it is not present in the current 
directory.[] 

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[]    \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s
",query->name);[] 

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[]    \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s
",target->name);[] 

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[]   \OT1/cmtt/m/n/10 * If the sequences are small enough then it should use ex
plicit memory.[] 
[13]
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[]  \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]
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[]    \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s
",query->name);[] 

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[]    \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s
",target->name);[] 

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[]   \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]
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[]    \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query
->name,target->name);[] 

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[]  \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp
,-gap,-ext);[] 

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[]    \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s
",query->name);[] 
[16]
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[]\OT1/cmtt/m/n/10 Q22037               EPENLRKIFVGGLTSNTTDDLMREFYSQFGEITDIIVMR
DPTTKRSRGF[] 

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[]                     \OT1/cmtt/m/n/10 EPE LRK+F+GGL+  TTD+ +R  + Q+G +TD +VMR
DP TKRSRGF[] 

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[]\OT1/cmtt/m/n/10 ROA1_HUMAN           EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMR
DPNTKRSRGF[] 

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[]\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,<state>) 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 <options> 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 <grin>. 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 <grin>. 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] <protein-seq> <protein-
fasta-database>\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)

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knappen/ec/tcrm1000.600pk></usr/share/texlive/texmf-dist/fonts/type1/public/ams
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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 <options> 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,<state>) 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 <options> 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 <grin>. 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 <grin>. 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))"[] 

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[]        \OT1/cmtt/m/n/10 For function CDNA\_BASE, you have arguments j and qu
ery, which do not[] 

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[]\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] <protein-seq> <protein-
fasta-database>\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[] 

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[]      \OT1/cmtt/m/n/10 either possible or how they are specified. Of course, 
there is the problem[] 

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[]      \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 )[] 

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[]    \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);[] 

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[]  \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)

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knappen/ec/tcrm1000.600pk></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmbx10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr
10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr12.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr17.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive
/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb>
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Transcript written on dynamite.log.
cd docs && pdflatex wise2.tex
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[2] [3] [4]

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[]\OT1/cmtt/m/n/10 This program is freely distributed under a GPL. See source d
irectory[] 

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[]\OT1/cmtt/m/n/10 Copyright (c) GRL limited: portions of the code are from sep
arate copyright[] 
[5]
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[]\OT1/cmtt/m/n/10 Warning: The bits scores is not probablistically correct for
 single seqs[] 

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[]\OT1/cmtt/m/n/10 roa1_drome        88 AQKSRPHKIDGRVVEPKRAVPRQ                
       DID[] 

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[]                     \OT1/cmtt/m/n/10 A  +RPHK+DGRVVEPKRAV R+                
       D[] 

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[]                     \OT1/cmtt/m/n/10 AMNARPHKVDGRVVEPKRAVSRE                
       DSQ[] 

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[]\OT1/cmtt/m/n/10 HSHNRNPA        1867 gaagaccagggagggcaaggtagGTGAGTG  Intron 
2   TAGgtc[] 

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[]                     \OT1/cmtt/m/n/10 ctacgcaataggttacagctcga<0-----[1936 : 2
083]-0>aca[] 

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[]                     \OT1/cmtt/m/n/10 tgtagacggtaatgaagatccaa                
       tta[] 

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[]\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[] 

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[]                     \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[] 

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[]                     \OT1/cmtt/m/n/10 aatccatgagatttctaactaatcaatttagtaatagta
cgtcactcga[] 

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[]\OT1/cmtt/m/n/10 roa1_drome       163 RGFAFVEFDDYDPVDKVV                     
     QKQHQ[] 

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[]                     \OT1/cmtt/m/n/10 RGFAFV FDD+D VDK+V                     
     QK H[] 
[6]
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[]                     \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[] 

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[]                     \OT1/cmtt/m/n/10 gctctactcctccgtgtc                     
     gactt[] 

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[]                     \OT1/cmtt/m/n/10 tagaagatgactcaaatcgcccgag <1-----[2481 
: 2793][] 
[7] [8]

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[9]

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[12]

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[15] [16] [17]

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[21]
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[]\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]
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[]\OT1/cmr/m/n/10 The half-wise pro-tein database, found at ftp://ftp.sanger.ac
.uk/pub/birney/wise2/halfwise 
[26]

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 []\OT1/cmtt/m/n/10 pexon <start-in-dna> <end-in-dna> <start-in-protein> <end-i
n-protein>[] 

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 []\OT1/cmtt/m/n/10 pexon <start-in-dna> <end-in-dna> <start-in-protein> <end-i
n-protein>[] 
[29]

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 []\OT1/cmtt/m/n/10 Bits   Query         start end Target      start end   idel
s introns[] 

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 []\OT1/cmtt/m/n/10 230.57 roa1_drome     26  347 HSHNRNPA     1386 3963    0  
  6[] 
[30] [31]

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[37] [38] [39] [40] [41] [42] (./wise2.aux)

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fonts/cm/cmbx10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr
10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr12.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr17.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive
/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb>
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
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(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
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(/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]
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[]\OT1/cmtt/m/n/10 This program is freely distributed under a GPL. See source d
irectory[] 

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[]\OT1/cmtt/m/n/10 Copyright (c) GRL limited: portions of the code are from sep
arate copyright[] 
[6]
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[]\OT1/cmtt/m/n/10 Warning: The bits scores is not probablistically correct for
 single seqs[] 

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[]\OT1/cmtt/m/n/10 roa1_drome        88 AQKSRPHKIDGRVVEPKRAVPRQ                
       DID[] 

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[]                     \OT1/cmtt/m/n/10 A  +RPHK+DGRVVEPKRAV R+                
       D[] 

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[]                     \OT1/cmtt/m/n/10 AMNARPHKVDGRVVEPKRAVSRE                
       DSQ[] 

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[]\OT1/cmtt/m/n/10 HSHNRNPA        1867 gaagaccagggagggcaaggtagGTGAGTG  Intron 
2   TAGgtc[] 

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[]                     \OT1/cmtt/m/n/10 ctacgcaataggttacagctcga<0-----[1936 : 2
083]-0>aca[] 

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[]                     \OT1/cmtt/m/n/10 tgtagacggtaatgaagatccaa                
       tta[] 

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[]\OT1/cmtt/m/n/10 roa1_drome       114 SPNAGATVKKLFVGALKDDHDEQSIRDYFQHFGNIVDIN
IVIDKETGKK[] 

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[]                      \OT1/cmtt/m/n/10 P A  TVKK+FVG +K+D +E  +RDYF+ +G I  I 
I+ D+ +GKK[] 

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[]                     \OT1/cmtt/m/n/10 RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIE
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[]                     \OT1/cmtt/m/n/10 RGFAFV FDD+D VDK+V                     
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[7]
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[]                     \OT1/cmtt/m/n/10 RGFAFVTFDDHDSVDKIV          L:I[att]   
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[]\OT1/cmtt/m/n/10 HSHNRNPA        2240 agtgtgatggcgtggaagAGTAAGTA  Intron 3   
TAGTTcatca[] 

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-1>  aaaac[] 

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     gactt[] 

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[]                     \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]
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[]\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]
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 []\OT1/cmtt/m/n/10 pexon <start-in-dna> <end-in-dna> <start-in-protein> <end-i
n-protein>[] 

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 []\OT1/cmtt/m/n/10 pexon <start-in-dna> <end-in-dna> <start-in-protein> <end-i
n-protein>[] 
[30]
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 []\OT1/cmtt/m/n/10 Bits   Query         start end Target      start end   idel
s introns[] 

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 []\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) </tmp/texfonts/pk/ljfour/j
knappen/ec/tcrm1000.600pk></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmbx10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr
10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr12.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr17.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive
/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb>
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 '/<<PKGBUILDDIR>>'
   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 '/<<PKGBUILDDIR>>'
	rm -f debian/wise.debhelper.log
   debian/rules override_dh_fixperms
make[1]: Entering directory '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
   dh_missing -a
   dh_dwz -a
	install -m0755 -d debian/wise/usr/lib/debug/.dwz/riscv64-linux-gnu
	dwz -mdebian/wise/usr/lib/debug/.dwz/riscv64-linux-gnu/wise.debug -M/usr/lib/debug/.dwz/riscv64-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
	riscv64-linux-gnu-objcopy --compress-debug-sections debian/wise/usr/lib/debug/.dwz/riscv64-linux-gnu/wise.debug
	chmod 0644 -- debian/wise/usr/lib/debug/.dwz/riscv64-linux-gnu/wise.debug
   dh_strip -a
	install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/11
	riscv64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genewisedb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/11/96dbff9bb54c79ecc65544a3147f9db80241b1.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/11/96dbff9bb54c79ecc65544a3147f9db80241b1.debug
	riscv64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genewisedb
	riscv64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/11/96dbff9bb54c79ecc65544a3147f9db80241b1.debug debian/wise/usr/bin/genewisedb
	install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/f0
	riscv64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/estwisedb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/f0/bfeb6b6221a41ea45f87ed503655face777111.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/f0/bfeb6b6221a41ea45f87ed503655face777111.debug
	riscv64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/estwisedb
	riscv64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/f0/bfeb6b6221a41ea45f87ed503655face777111.debug debian/wise/usr/bin/estwisedb
	install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/ea
	riscv64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genewise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/ea/c389bd0f4ccdadbe5057ddc53d060ad7071a5a.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/ea/c389bd0f4ccdadbe5057ddc53d060ad7071a5a.debug
	riscv64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genewise
	riscv64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/ea/c389bd0f4ccdadbe5057ddc53d060ad7071a5a.debug debian/wise/usr/bin/genewise
	install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/04
	riscv64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/estwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/04/d7cdb1365f8797a3e7dbc5c6957315b4eb1b4b.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/04/d7cdb1365f8797a3e7dbc5c6957315b4eb1b4b.debug
	riscv64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/estwise
	riscv64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/04/d7cdb1365f8797a3e7dbc5c6957315b4eb1b4b.debug debian/wise/usr/bin/estwise
	install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/1e
	riscv64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/scanwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/1e/c749b8173e0a0a09f1d2bb22f09b13879f01fb.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/1e/c749b8173e0a0a09f1d2bb22f09b13879f01fb.debug
	riscv64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/scanwise
	riscv64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/1e/c749b8173e0a0a09f1d2bb22f09b13879f01fb.debug debian/wise/usr/bin/scanwise
	install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a6
	riscv64-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/a6/ef77de747061fd964efaf0f29963b4238346ce.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a6/ef77de747061fd964efaf0f29963b4238346ce.debug
	riscv64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/scanwise_server
	riscv64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a6/ef77de747061fd964efaf0f29963b4238346ce.debug debian/wise/usr/bin/scanwise_server
	install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/be
	riscv64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/pswdb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/be/80bbd6c59a99c9400bf3dd20e40f64957bcf9e.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/be/80bbd6c59a99c9400bf3dd20e40f64957bcf9e.debug
	riscv64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/pswdb
	riscv64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/be/80bbd6c59a99c9400bf3dd20e40f64957bcf9e.debug debian/wise/usr/bin/pswdb
	install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/75
	riscv64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/psw debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/75/4d0f28c8349ad80de3e73d6a71676764e2c19f.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/75/4d0f28c8349ad80de3e73d6a71676764e2c19f.debug
	riscv64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/psw
	riscv64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/75/4d0f28c8349ad80de3e73d6a71676764e2c19f.debug debian/wise/usr/bin/psw
	install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/bf
	riscv64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/promoterwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/bf/00e84fed20c39c8833e1ffd12ffd8e2717dc1f.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/bf/00e84fed20c39c8833e1ffd12ffd8e2717dc1f.debug
	riscv64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/promoterwise
	riscv64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/bf/00e84fed20c39c8833e1ffd12ffd8e2717dc1f.debug debian/wise/usr/bin/promoterwise
	install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/18
	riscv64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genomewise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/18/6eeca6e3d3db53a291faeb158df443f045e855.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/18/6eeca6e3d3db53a291faeb158df443f045e855.debug
	riscv64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genomewise
	riscv64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/18/6eeca6e3d3db53a291faeb158df443f045e855.debug debian/wise/usr/bin/genomewise
	install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fc
	riscv64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/dba debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fc/9c5e23697234e9fb6f48fe80bfd7a07d6e552e.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fc/9c5e23697234e9fb6f48fe80bfd7a07d6e552e.debug
	riscv64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/dba
	riscv64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fc/9c5e23697234e9fb6f48fe80bfd7a07d6e552e.debug debian/wise/usr/bin/dba
	install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/13
	riscv64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/dnal debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/13/e1b649e4a60b3be0b8a90aacbcc123e82d50f0.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/13/e1b649e4a60b3be0b8a90aacbcc123e82d50f0.debug
	riscv64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/dnal
	riscv64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/13/e1b649e4a60b3be0b8a90aacbcc123e82d50f0.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/riscv64-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/estwisedb debian/wise/usr/bin/genewise 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
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
 diversion by libc6 from: /lib/ld-linux-riscv64-lp64d.so.1
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
 diversion by libc6 to: /lib/ld-linux-riscv64-lp64d.so.1.usr-is-merged
   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="04d7cdb1365f8797a3e7dbc5c6957315b4eb1b4b 1196dbff9bb54c79ecc65544a3147f9db80241b1 13e1b649e4a60b3be0b8a90aacbcc123e82d50f0 186eeca6e3d3db53a291faeb158df443f045e855 1ec749b8173e0a0a09f1d2bb22f09b13879f01fb 754d0f28c8349ad80de3e73d6a71676764e2c19f a6ef77de747061fd964efaf0f29963b4238346ce be80bbd6c59a99c9400bf3dd20e40f64957bcf9e bf00e84fed20c39c8833e1ffd12ffd8e2717dc1f eac389bd0f4ccdadbe5057ddc53d060ad7071a5a f0bfeb6b6221a41ea45f87ed503655face777111 fc9c5e23697234e9fb6f48fe80bfd7a07d6e552e" -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_riscv64.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_riscv64.deb'.
 dpkg-genbuildinfo --build=any -O../wise_2.4.1-28_riscv64.buildinfo
 dpkg-genchanges --build=any -O../wise_2.4.1-28_riscv64.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 2026-02-22T11:08:53Z

+------------------------------------------------------------------------------+
| Finished Timed Build Commands                                                |
+------------------------------------------------------------------------------+


rm -Rf /<<PKGBUILDDIR>>/
-------------------------------------


I: Finished running 'rm -Rf /<<PKGBUILDDIR>>/'.

Finished processing commands.
--------------------------------------------------------------------------------

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Changes                                                                      |
+------------------------------------------------------------------------------+


wise_2.4.1-28_riscv64.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: riscv64
Version: 2.4.1-28
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Santiago Vila <sanvila@debian.org>
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:
 544fde2cad7a5cdfaba68e5e1af64f9f56efa53e 9628656 wise-dbgsym_2.4.1-28_riscv64.deb
 7d49b2594cc6279e0e18b0bcbc49c9d3124276c1 10087 wise_2.4.1-28_riscv64.buildinfo
 4a1363c156ac3b9f56752d6f085e34fd2a50d57c 1129196 wise_2.4.1-28_riscv64.deb
Checksums-Sha256:
 d1d46d078a1b823f141581c68dd7d2b1b1a26b7a1bee53efadd1af1960e15cc0 9628656 wise-dbgsym_2.4.1-28_riscv64.deb
 f661d6ad03af4a5158ec02781d80918adee2e8c9105023c43d37e10ebd568f82 10087 wise_2.4.1-28_riscv64.buildinfo
 ecf66ef7e01720ea7424d69e453190114f19f2143f3397f6c8f7d55b7c394192 1129196 wise_2.4.1-28_riscv64.deb
Files:
 9ba80ac570b92e63b07c1da3e488a72f 9628656 debug optional wise-dbgsym_2.4.1-28_riscv64.deb
 e7d2f54631f00d1c5a8961250143f1be 10087 science optional wise_2.4.1-28_riscv64.buildinfo
 455db1d2d0ab4f0faef39a8cd2f878d9 1129196 science optional wise_2.4.1-28_riscv64.deb

+------------------------------------------------------------------------------+
| Buildinfo                                                                    |
+------------------------------------------------------------------------------+

Format: 1.0
Source: wise
Binary: wise wise-dbgsym
Architecture: riscv64
Version: 2.4.1-28
Checksums-Md5:
 9ba80ac570b92e63b07c1da3e488a72f 9628656 wise-dbgsym_2.4.1-28_riscv64.deb
 455db1d2d0ab4f0faef39a8cd2f878d9 1129196 wise_2.4.1-28_riscv64.deb
Checksums-Sha1:
 544fde2cad7a5cdfaba68e5e1af64f9f56efa53e 9628656 wise-dbgsym_2.4.1-28_riscv64.deb
 4a1363c156ac3b9f56752d6f085e34fd2a50d57c 1129196 wise_2.4.1-28_riscv64.deb
Checksums-Sha256:
 d1d46d078a1b823f141581c68dd7d2b1b1a26b7a1bee53efadd1af1960e15cc0 9628656 wise-dbgsym_2.4.1-28_riscv64.deb
 ecf66ef7e01720ea7424d69e453190114f19f2143f3397f6c8f7d55b7c394192 1129196 wise_2.4.1-28_riscv64.deb
Build-Origin: Debian
Build-Architecture: amd64
Build-Date: Sun, 22 Feb 2026 11:08:53 +0000
Build-Path: /<<PKGBUILDDIR>>
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_riscv64.deb
--------------------------------

 new Debian package, version 2.0.
 size 9628656 bytes: control archive=1136 bytes.
     815 bytes,    12 lines      control
    1354 bytes,    13 lines      md5sums
 Package: wise-dbgsym
 Source: wise
 Version: 2.4.1-28
 Auto-Built-Package: debug-symbols
 Architecture: riscv64
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 18779
 Depends: wise (= 2.4.1-28)
 Section: debug
 Priority: optional
 Description: debug symbols for wise
 Build-Ids: 04d7cdb1365f8797a3e7dbc5c6957315b4eb1b4b 1196dbff9bb54c79ecc65544a3147f9db80241b1 13e1b649e4a60b3be0b8a90aacbcc123e82d50f0 186eeca6e3d3db53a291faeb158df443f045e855 1ec749b8173e0a0a09f1d2bb22f09b13879f01fb 754d0f28c8349ad80de3e73d6a71676764e2c19f a6ef77de747061fd964efaf0f29963b4238346ce be80bbd6c59a99c9400bf3dd20e40f64957bcf9e bf00e84fed20c39c8833e1ffd12ffd8e2717dc1f eac389bd0f4ccdadbe5057ddc53d060ad7071a5a f0bfeb6b6221a41ea45f87ed503655face777111 fc9c5e23697234e9fb6f48fe80bfd7a07d6e552e

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/lib/
drwxr-xr-x root/root         0 2026-02-19 20:03 ./usr/lib/debug/
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drwxr-xr-x root/root         0 2026-02-19 20:03 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root         0 2026-02-19 20:03 ./usr/lib/debug/.dwz/riscv64-linux-gnu/
-rw-r--r-- root/root    100104 2026-02-19 20:03 ./usr/lib/debug/.dwz/riscv64-linux-gnu/wise.debug
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/
lrwxrwxrwx root/root         0 2026-02-19 20:03 ./usr/share/doc/wise-dbgsym -> wise


wise_2.4.1-28_riscv64.deb
-------------------------

 new Debian package, version 2.0.
 size 1129196 bytes: control archive=1968 bytes.
    1725 bytes,    33 lines      control
    1742 bytes,    29 lines      md5sums
 Package: wise
 Version: 2.4.1-28
 Architecture: riscv64
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 8160
 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.

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drwxr-xr-x root/root         0 2026-02-19 20:03 ./usr/bin/
-rwxr-xr-x root/root    268688 2026-02-19 20:03 ./usr/bin/dba
-rwxr-xr-x root/root    186696 2026-02-19 20:03 ./usr/bin/dnal
-rwxr-xr-x root/root   1524120 2026-02-19 20:03 ./usr/bin/estwise
-rwxr-xr-x root/root   1528320 2026-02-19 20:03 ./usr/bin/estwisedb
-rwxr-xr-x root/root   1528312 2026-02-19 20:03 ./usr/bin/genewise
-rwxr-xr-x root/root   1532480 2026-02-19 20:03 ./usr/bin/genewisedb
-rwxr-xr-x root/root    301384 2026-02-19 20:03 ./usr/bin/genomewise
-rwxr-xr-x root/root    330056 2026-02-19 20:03 ./usr/bin/promoterwise
-rwxr-xr-x root/root    272712 2026-02-19 20:03 ./usr/bin/psw
-rwxr-xr-x root/root    276888 2026-02-19 20:03 ./usr/bin/pswdb
-rwxr-xr-x root/root    399688 2026-02-19 20:03 ./usr/bin/scanwise
-rwxr-xr-x root/root    166208 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 /<<RESOLVERDIR>>/sbuild-build-depends-lintian-dummy has unusual owner or group 1000:119
dpkg-deb: hint: you might need to pass --root-owner-group, see <https://wiki.debian.org/Teams/Dpkg/RootlessBuilds> for further details
dpkg-deb: warning: ignoring 1 warning about the control file(s)
dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-lintian-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [615 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [1393 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [1476 B]
Fetched 3484 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:riscv64
  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:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [852 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 ...
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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) ...
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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) ...
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Setting up libnghttp2-14:amd64 (1.68.0-1) ...
Setting up perl-openssl-defaults:amd64 (7+b2) ...
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Setting up libxml-namespacesupport-perl (1.12-2) ...
Setting up libgcrypt20:amd64 (1.11.2-3+b1) ...
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Setting up patchutils (0.4.3-1) ...
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Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3+b1) ...
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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) ...
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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) ...
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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:riscv64 (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                                                                   |
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+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: amd64
Build Profiles: cross nocheck
Build Type: any
Build-Space: n/a
Build-Time: 151
Distribution: unstable
Foreign Architectures: riscv64
Host Architecture: riscv64
Install-Time: 50
Job: wise_2.4.1-28
Lintian: pass
Machine Architecture: amd64
Package: wise
Package-Time: 210
Source-Version: 2.4.1-28
Space: n/a
Status: successful
Version: 2.4.1-28
--------------------------------------------------------------------------------
Finished at 2026-02-22T11:08:53Z
Build needed 00:03:30, no disk space