sbuild (Debian sbuild) 0.78.1 (09 February 2019) on mjolnir

+==============================================================================+
| wise 2.4.1-23 (amd64)                        Sat, 17 Jul 2021 08:10:28 +0000 |
+==============================================================================+

Package: wise
Version: 2.4.1-23
Source Version: 2.4.1-23
Distribution: unstable
Machine Architecture: arm64
Host Architecture: amd64
Build Architecture: arm64
Build Profiles: cross nocheck
Build Type: any

I: NOTICE: Log filtering will replace 'var/run/schroot/mount/crossqa-sid-55208159-d16b-4353-8054-8294b5eb239f' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/wise-JXXKWt/resolver-M9fRWn' with '<<RESOLVERDIR>>'

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

Hit:1 http://mirror.einval.org/debian sid InRelease
Get:2 http://mirror.einval.org/debian sid/main amd64 Packages [8638 kB]
Fetched 8638 kB in 3s (3371 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

+------------------------------------------------------------------------------+
| Fetch source files                                                           |
+------------------------------------------------------------------------------+


Check APT
---------

Checking available source versions...

Download source files with APT
------------------------------

Reading package lists...
NOTICE: 'wise' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/wise.git
Please use:
git clone https://salsa.debian.org/med-team/wise.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 3440 kB of source archives.
Get:1 http://mirror.einval.org/debian sid/main wise 2.4.1-23 (dsc) [2179 B]
Get:2 http://mirror.einval.org/debian sid/main wise 2.4.1-23 (tar) [3410 kB]
Get:3 http://mirror.einval.org/debian sid/main wise 2.4.1-23 (diff) [27.2 kB]
Fetched 3440 kB in 0s (36.2 MB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/wise-JXXKWt/wise-2.4.1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/wise-JXXKWt' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: debhelper-compat (= 12), texlive-latex-base, texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev, libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-amd64:arm64, libc-dev:amd64, libstdc++-dev:amd64
Filtered Build-Depends: debhelper-compat (= 12), texlive-latex-base, texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev, libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-amd64:arm64, libc-dev:amd64, libstdc++-dev:amd64
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 [957 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [446 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [536 B]
Fetched 1939 B in 0s (45.9 kB/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...
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev binutils-x86-64-linux-gnu
  bsdextrautils cpp-10-x86-64-linux-gnu cpp-x86-64-linux-gnu cross-config
  crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism
  docbook docbook-to-man dpkg-cross dwz file fontconfig-config
  fonts-dejavu-core fonts-lmodern fonts-urw-base35 g++-10-x86-64-linux-gnu
  g++-x86-64-linux-gnu gcc-10-base:amd64 gcc-10-cross-base
  gcc-10-x86-64-linux-gnu gcc-10-x86-64-linux-gnu-base gcc-x86-64-linux-gnu
  gettext gettext-base ghostscript groff-base hevea intltool-debian
  libarchive-zip-perl libasan6:amd64 libasan6-amd64-cross libatomic1:amd64
  libatomic1-amd64-cross libavahi-client3 libavahi-common-data
  libavahi-common3 libblkid-dev:amd64 libblkid1:amd64 libbrotli1 libbsd0
  libc6:amd64 libc6-amd64-cross libc6-dev:amd64 libc6-dev-amd64-cross
  libcairo2 libcom-err2:amd64 libconfig-auto-perl libconfig-inifiles-perl
  libcrypt-dev:amd64 libcrypt1:amd64 libcups2 libdatrie1 libdbus-1-3
  libdebhelper-perl libdebian-dpkgcross-perl libdeflate0 libelf1 libexpat1
  libffi-dev:amd64 libffi7:amd64 libfile-homedir-perl
  libfile-stripnondeterminism-perl libfile-which-perl libfontconfig1
  libfontenc1 libfreetype6 libgcc-10-dev:amd64 libgcc-10-dev-amd64-cross
  libgcc-s1:amd64 libgcc-s1-amd64-cross libglib2.0-0 libglib2.0-0:amd64
  libglib2.0-bin libglib2.0-data libglib2.0-dev:amd64 libglib2.0-dev-bin
  libgomp1:amd64 libgomp1-amd64-cross libgraphite2-3 libgs9 libgs9-common
  libgssapi-krb5-2:amd64 libharfbuzz0b libice6 libicu67 libidn11 libijs-0.35
  libio-string-perl libitm1:amd64 libitm1-amd64-cross libjbig0 libjbig2dec0
  libjpeg62-turbo libjs-jquery libk5crypto3:amd64 libkeyutils1:amd64
  libkpathsea6 libkrb5-3:amd64 libkrb5support0:amd64 liblcms2-2
  liblocale-gettext-perl liblsan0:amd64 liblsan0-amd64-cross libmagic-mgc
  libmagic1 libmd0 libmime-charset-perl libmount-dev:amd64 libmount1:amd64
  libmpdec3 libncursesw6 libnetpbm10 libnsl-dev:amd64 libnsl2:amd64
  libopenjp2-7 libosp5 libpaper-utils libpaper1 libpcre16-3:amd64
  libpcre2-16-0:amd64 libpcre2-32-0:amd64 libpcre2-8-0:amd64
  libpcre2-dev:amd64 libpcre2-posix2:amd64 libpcre3:amd64 libpcre3-dev:amd64
  libpcre32-3:amd64 libpcrecpp0v5:amd64 libpipeline1 libpixman-1-0 libpng16-16
  libptexenc1 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib
  libquadmath0:amd64 libquadmath0-amd64-cross libreadline8 libselinux1:amd64
  libselinux1-dev:amd64 libsepol1:amd64 libsepol1-dev:amd64 libsigsegv2 libsm6
  libsombok3 libsqlite3-0 libssl1.1:amd64 libstdc++-10-dev:amd64
  libstdc++-10-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross
  libsub-override-perl libsynctex2 libteckit0 libtexlua53 libthai-data
  libthai0 libtiff5 libtirpc-dev:amd64 libtirpc3:amd64 libtool libtsan0:amd64
  libtsan0-amd64-cross libubsan1:amd64 libubsan1-amd64-cross libuchardet0
  libunicode-linebreak-perl libuuid1:amd64 libwebp6 libx11-6 libx11-data
  libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6
  libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl
  libxml-sax-perl libxml-simple-perl libxml2 libxmu6 libxpm4 libxrender1
  libxt6 libyaml-perl libzzip-0-13 linux-libc-dev:amd64
  linux-libc-dev-amd64-cross lmodern m4 man-db media-types netpbm opensp
  pkg-config po-debconf poppler-data python3 python3-distutils python3-lib2to3
  python3-minimal python3.9 python3.9-minimal readline-common sensible-utils
  sgml-base sgml-data t1utils tex-common texlive-base texlive-binaries
  texlive-extra-utils texlive-latex-base texlive-luatex texlive-plain-generic
  ucf uuid-dev:amd64 x11-common xdg-utils xfonts-encodings xfonts-utils
  xml-core zlib1g:amd64 zlib1g-dev:amd64
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-10-locales
  cpp-doc dh-make docbook-defguide docbook-dsssl docbook-xml psgml
  binutils-multiarch fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre
  g++-10-multilib-x86-64-linux-gnu gcc-10-doc gcc-10-multilib-x86-64-linux-gnu
  manpages-dev flex bison gdb-x86-64-linux-gnu gcc-doc gettext-doc
  libasprintf-dev libgettextpo-dev ghostscript-x groff hevea-doc
  texlive-latex-extra glibc-doc:amd64 libc-l10n:amd64 locales:amd64
  manpages-dev:amd64 cups-common libgirepository1.0-dev:amd64
  libglib2.0-doc:amd64 libgdk-pixbuf2.0-bin | libgdk-pixbuf2.0-dev
  libxml2-utils krb5-doc:amd64 krb5-user:amd64 liblcms2-utils
  libencode-hanextra-perl libpod2-base-perl libstdc++-10-doc:amd64 libtool-doc
  gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor
  less www-browser doc-base libmail-box-perl poppler-utils
  fonts-japanese-mincho | fonts-ipafont-mincho fonts-japanese-gothic
  | fonts-ipafont-gothic fonts-arphic-ukai fonts-arphic-uming fonts-nanum
  python3-doc python3-tk python3-venv python3.9-venv python3.9-doc
  binfmt-support readline-doc sgml-base-doc perlsgml w3-recs perl-tk xpdf
  | pdf-viewer xzdec chktex default-jre-headless dvidvi dvipng fragmaster
  lacheck latexdiff latexmk purifyeps xindy texlive-latex-base-doc
Recommended packages:
  curl | wget | lynx libidn2-0:amd64 libnss-nis:amd64 libnss-nisplus:amd64
  dbus libarchive-cpio-perl shared-mime-info xdg-user-dirs
  shared-mime-info:amd64 xdg-user-dirs:amd64 fonts-droid-fallback
  javascript-common krb5-locales:amd64 libgpm2 ca-certificates libltdl-dev
  uuid-runtime:amd64 libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl
  | libyaml-syck-perl libmail-sendmail-perl dvisvgm liblog-log4perl-perl
  libyaml-tiny-perl ruby | ruby-interpreter 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-x86-64-linux-gnu
  bsdextrautils cpp-10-x86-64-linux-gnu cpp-x86-64-linux-gnu cross-config
  crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism
  docbook docbook-to-man dpkg-cross dwz file fontconfig-config
  fonts-dejavu-core fonts-lmodern fonts-urw-base35 g++-10-x86-64-linux-gnu
  g++-x86-64-linux-gnu gcc-10-base:amd64 gcc-10-cross-base
  gcc-10-x86-64-linux-gnu gcc-10-x86-64-linux-gnu-base gcc-x86-64-linux-gnu
  gettext gettext-base ghostscript groff-base hevea intltool-debian
  libarchive-zip-perl libasan6:amd64 libasan6-amd64-cross libatomic1:amd64
  libatomic1-amd64-cross libavahi-client3 libavahi-common-data
  libavahi-common3 libblkid-dev:amd64 libblkid1:amd64 libbrotli1 libbsd0
  libc6:amd64 libc6-amd64-cross libc6-dev:amd64 libc6-dev-amd64-cross
  libcairo2 libcom-err2:amd64 libconfig-auto-perl libconfig-inifiles-perl
  libcrypt-dev:amd64 libcrypt1:amd64 libcups2 libdatrie1 libdbus-1-3
  libdebhelper-perl libdebian-dpkgcross-perl libdeflate0 libelf1 libexpat1
  libffi-dev:amd64 libffi7:amd64 libfile-homedir-perl
  libfile-stripnondeterminism-perl libfile-which-perl libfontconfig1
  libfontenc1 libfreetype6 libgcc-10-dev:amd64 libgcc-10-dev-amd64-cross
  libgcc-s1:amd64 libgcc-s1-amd64-cross libglib2.0-0 libglib2.0-0:amd64
  libglib2.0-bin libglib2.0-data libglib2.0-dev:amd64 libglib2.0-dev-bin
  libgomp1:amd64 libgomp1-amd64-cross libgraphite2-3 libgs9 libgs9-common
  libgssapi-krb5-2:amd64 libharfbuzz0b libice6 libicu67 libidn11 libijs-0.35
  libio-string-perl libitm1:amd64 libitm1-amd64-cross libjbig0 libjbig2dec0
  libjpeg62-turbo libjs-jquery libk5crypto3:amd64 libkeyutils1:amd64
  libkpathsea6 libkrb5-3:amd64 libkrb5support0:amd64 liblcms2-2
  liblocale-gettext-perl liblsan0:amd64 liblsan0-amd64-cross libmagic-mgc
  libmagic1 libmd0 libmime-charset-perl libmount-dev:amd64 libmount1:amd64
  libmpdec3 libncursesw6 libnetpbm10 libnsl-dev:amd64 libnsl2:amd64
  libopenjp2-7 libosp5 libpaper-utils libpaper1 libpcre16-3:amd64
  libpcre2-16-0:amd64 libpcre2-32-0:amd64 libpcre2-8-0:amd64
  libpcre2-dev:amd64 libpcre2-posix2:amd64 libpcre3:amd64 libpcre3-dev:amd64
  libpcre32-3:amd64 libpcrecpp0v5:amd64 libpipeline1 libpixman-1-0 libpng16-16
  libptexenc1 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib
  libquadmath0:amd64 libquadmath0-amd64-cross libreadline8 libselinux1:amd64
  libselinux1-dev:amd64 libsepol1:amd64 libsepol1-dev:amd64 libsigsegv2 libsm6
  libsombok3 libsqlite3-0 libssl1.1:amd64 libstdc++-10-dev:amd64
  libstdc++-10-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross
  libsub-override-perl libsynctex2 libteckit0 libtexlua53 libthai-data
  libthai0 libtiff5 libtirpc-dev:amd64 libtirpc3:amd64 libtool libtsan0:amd64
  libtsan0-amd64-cross libubsan1:amd64 libubsan1-amd64-cross libuchardet0
  libunicode-linebreak-perl libuuid1:amd64 libwebp6 libx11-6 libx11-data
  libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxi6
  libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl
  libxml-sax-perl libxml-simple-perl libxml2 libxmu6 libxpm4 libxrender1
  libxt6 libyaml-perl libzzip-0-13 linux-libc-dev:amd64
  linux-libc-dev-amd64-cross lmodern m4 man-db media-types netpbm opensp
  pkg-config po-debconf poppler-data python3 python3-distutils python3-lib2to3
  python3-minimal python3.9 python3.9-minimal readline-common
  sbuild-build-depends-main-dummy:amd64 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:amd64
  x11-common xdg-utils xfonts-encodings xfonts-utils xml-core zlib1g:amd64
  zlib1g-dev:amd64
0 upgraded, 237 newly installed, 0 to remove and 0 not upgraded.
Need to get 391 MB of archives.
After this operation, 1400 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [964 B]
Get:2 http://mirror.einval.org/debian sid/main arm64 bsdextrautils arm64 2.36.1-7 [141 kB]
Get:3 http://mirror.einval.org/debian sid/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB]
Get:4 http://mirror.einval.org/debian sid/main arm64 groff-base arm64 1.22.4-6 [883 kB]
Get:5 http://mirror.einval.org/debian sid/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB]
Get:6 http://mirror.einval.org/debian sid/main arm64 man-db arm64 2.9.4-2 [1336 kB]
Get:7 http://mirror.einval.org/debian sid/main arm64 liblocale-gettext-perl arm64 1.07-4+b1 [18.9 kB]
Get:8 http://mirror.einval.org/debian sid/main arm64 poppler-data all 0.4.10-1 [1602 kB]
Get:9 http://mirror.einval.org/debian sid/main arm64 libpython3.9-minimal arm64 3.9.2-1 [797 kB]
Get:10 http://mirror.einval.org/debian sid/main arm64 libexpat1 arm64 2.2.10-2 [83.1 kB]
Get:11 http://mirror.einval.org/debian sid/main arm64 python3.9-minimal arm64 3.9.2-1 [1884 kB]
Get:12 http://mirror.einval.org/debian sid/main arm64 python3-minimal arm64 3.9.2-3 [38.2 kB]
Get:13 http://mirror.einval.org/debian sid/main arm64 media-types all 4.0.0 [30.3 kB]
Get:14 http://mirror.einval.org/debian sid/main arm64 libmpdec3 arm64 2.5.1-2 [84.4 kB]
Get:15 http://mirror.einval.org/debian sid/main arm64 libncursesw6 arm64 6.2+20201114-2 [121 kB]
Get:16 http://mirror.einval.org/debian sid/main arm64 readline-common all 8.1-2 [73.8 kB]
Get:17 http://mirror.einval.org/debian sid/main arm64 libreadline8 arm64 8.1-2 [160 kB]
Get:18 http://mirror.einval.org/debian sid/main arm64 libsqlite3-0 arm64 3.34.1-3 [750 kB]
Get:19 http://mirror.einval.org/debian sid/main arm64 libpython3.9-stdlib arm64 3.9.2-1 [1658 kB]
Get:20 http://mirror.einval.org/debian sid/main arm64 python3.9 arm64 3.9.2-1 [466 kB]
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Get:22 http://mirror.einval.org/debian sid/main arm64 python3 arm64 3.9.2-3 [37.9 kB]
Get:23 http://mirror.einval.org/debian sid/main arm64 sgml-base all 1.30 [15.1 kB]
Get:24 http://mirror.einval.org/debian sid/main arm64 sensible-utils all 0.0.14 [14.8 kB]
Get:25 http://mirror.einval.org/debian sid/main arm64 ucf all 3.0043 [74.0 kB]
Get:26 http://mirror.einval.org/debian sid/main arm64 tex-common all 6.16 [53.7 kB]
Get:27 http://mirror.einval.org/debian sid/main amd64 gcc-10-base amd64 10.2.1-6 [201 kB]
Get:28 http://mirror.einval.org/debian sid/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB]
Get:29 http://mirror.einval.org/debian sid/main arm64 libmagic1 arm64 1:5.39-3 [121 kB]
Get:30 http://mirror.einval.org/debian sid/main arm64 file arm64 1:5.39-3 [69.1 kB]
Get:31 http://mirror.einval.org/debian sid/main arm64 gettext-base arm64 0.21-4 [173 kB]
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Get:33 http://mirror.einval.org/debian sid/main arm64 m4 arm64 1.4.18-5 [199 kB]
Get:34 http://mirror.einval.org/debian sid/main arm64 autoconf all 2.69-14 [313 kB]
Get:35 http://mirror.einval.org/debian sid/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:36 http://mirror.einval.org/debian sid/main arm64 automake all 1:1.16.3-2 [814 kB]
Get:37 http://mirror.einval.org/debian sid/main arm64 autopoint all 0.21-4 [510 kB]
Get:38 http://mirror.einval.org/debian sid/main arm64 gcc-10-x86-64-linux-gnu-base arm64 10.2.1-6cross1 [202 kB]
Get:39 http://mirror.einval.org/debian sid/main arm64 cpp-10-x86-64-linux-gnu arm64 10.2.1-6cross1 [46.2 MB]
Get:40 http://mirror.einval.org/debian sid/main arm64 cpp-x86-64-linux-gnu arm64 4:10.2.1-1 [16.8 kB]
Get:41 http://mirror.einval.org/debian sid/main arm64 cross-config all 2.6.18+nmu1 [31.5 kB]
Get:42 http://mirror.einval.org/debian sid/main arm64 binutils-x86-64-linux-gnu arm64 2.35.2-2 [1966 kB]
Get:43 http://mirror.einval.org/debian sid/main arm64 gcc-10-cross-base all 10.2.1-6cross1 [197 kB]
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Get:46 http://mirror.einval.org/debian sid/main arm64 libitm1-amd64-cross all 10.2.1-6cross1 [25.3 kB]
Get:47 http://mirror.einval.org/debian sid/main arm64 libatomic1-amd64-cross all 10.2.1-6cross1 [8752 B]
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Get:56 http://mirror.einval.org/debian sid/main arm64 gcc-10-x86-64-linux-gnu arm64 10.2.1-6cross1 [52.2 MB]
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Get:61 http://mirror.einval.org/debian sid/main arm64 g++-10-x86-64-linux-gnu arm64 10.2.1-6cross1 [49.2 MB]
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Get:63 http://mirror.einval.org/debian sid/main arm64 libconfig-inifiles-perl all 3.000003-1 [52.1 kB]
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Get:65 http://mirror.einval.org/debian sid/main arm64 libicu67 arm64 67.1-7 [8467 kB]
Get:66 http://mirror.einval.org/debian sid/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB]
Get:67 http://mirror.einval.org/debian sid/main arm64 libxml-namespacesupport-perl all 1.12-1.1 [14.9 kB]
Get:68 http://mirror.einval.org/debian sid/main arm64 libxml-sax-base-perl all 1.09-1.1 [20.7 kB]
Get:69 http://mirror.einval.org/debian sid/main arm64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB]
Get:70 http://mirror.einval.org/debian sid/main arm64 libxml-libxml-perl arm64 2.0134+dfsg-2+b1 [326 kB]
Get:71 http://mirror.einval.org/debian sid/main arm64 libxml-simple-perl all 2.25-1 [72.0 kB]
Get:72 http://mirror.einval.org/debian sid/main arm64 libyaml-perl all 1.30-1 [67.7 kB]
Get:73 http://mirror.einval.org/debian sid/main arm64 libconfig-auto-perl all 0.44-1.1 [19.0 kB]
Get:74 http://mirror.einval.org/debian sid/main arm64 libfile-which-perl all 1.23-1 [16.6 kB]
Get:75 http://mirror.einval.org/debian sid/main arm64 libfile-homedir-perl all 1.006-1 [43.8 kB]
Get:76 http://mirror.einval.org/debian sid/main arm64 libdebian-dpkgcross-perl all 2.6.18+nmu1 [30.5 kB]
Get:77 http://mirror.einval.org/debian sid/main arm64 dpkg-cross all 2.6.18+nmu1 [41.6 kB]
Get:78 http://mirror.einval.org/debian sid/main arm64 crossbuild-essential-amd64 all 12.9 [6708 B]
Get:79 http://mirror.einval.org/debian sid/main arm64 libdebhelper-perl all 13.3.4 [189 kB]
Get:80 http://mirror.einval.org/debian sid/main arm64 libtool all 2.4.6-15 [513 kB]
Get:81 http://mirror.einval.org/debian sid/main arm64 dh-autoreconf all 20 [17.1 kB]
Get:82 http://mirror.einval.org/debian sid/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get:83 http://mirror.einval.org/debian sid/main arm64 libsub-override-perl all 0.09-2 [10.2 kB]
Get:84 http://mirror.einval.org/debian sid/main arm64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB]
Get:85 http://mirror.einval.org/debian sid/main arm64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB]
Get:86 http://mirror.einval.org/debian sid/main arm64 libelf1 arm64 0.183-3 [164 kB]
Get:87 http://mirror.einval.org/debian sid/main arm64 dwz arm64 0.14-1 [90.0 kB]
Get:88 http://mirror.einval.org/debian sid/main arm64 gettext arm64 0.21-4 [1261 kB]
Get:89 http://mirror.einval.org/debian sid/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:90 http://mirror.einval.org/debian sid/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get:91 http://mirror.einval.org/debian sid/main arm64 debhelper all 13.3.4 [1049 kB]
Get:92 http://mirror.einval.org/debian sid/main arm64 xml-core all 0.18+nmu1 [23.8 kB]
Get:93 http://mirror.einval.org/debian sid/main arm64 sgml-data all 2.0.11+nmu1 [179 kB]
Get:94 http://mirror.einval.org/debian sid/main arm64 docbook all 4.5-6 [129 kB]
Get:95 http://mirror.einval.org/debian sid/main arm64 libosp5 arm64 1.5.2-13+b2 [884 kB]
Get:96 http://mirror.einval.org/debian sid/main arm64 opensp arm64 1.5.2-13+b2 [414 kB]
Get:97 http://mirror.einval.org/debian sid/main arm64 docbook-to-man arm64 1:2.0.0-45 [75.6 kB]
Get:98 http://mirror.einval.org/debian sid/main arm64 fonts-dejavu-core all 2.37-2 [1069 kB]
Get:99 http://mirror.einval.org/debian sid/main arm64 fonts-urw-base35 all 20200910-1 [6367 kB]
Get:100 http://mirror.einval.org/debian sid/main arm64 fontconfig-config all 2.13.1-4.2 [281 kB]
Get:101 http://mirror.einval.org/debian sid/main arm64 fonts-lmodern all 2.004.5-6.1 [4540 kB]
Get:102 http://mirror.einval.org/debian sid/main arm64 libgs9-common all 9.53.3~dfsg-7 [734 kB]
Get:103 http://mirror.einval.org/debian sid/main arm64 libavahi-common-data arm64 0.8-5 [123 kB]
Get:104 http://mirror.einval.org/debian sid/main arm64 libavahi-common3 arm64 0.8-5 [57.1 kB]
Get:105 http://mirror.einval.org/debian sid/main arm64 libdbus-1-3 arm64 1.12.20-2 [208 kB]
Get:106 http://mirror.einval.org/debian sid/main arm64 libavahi-client3 arm64 0.8-5 [60.6 kB]
Get:107 http://mirror.einval.org/debian sid/main arm64 libcups2 arm64 2.3.3op2-3+deb11u1 [334 kB]
Get:108 http://mirror.einval.org/debian sid/main arm64 libbrotli1 arm64 1.0.9-2+b2 [267 kB]
Get:109 http://mirror.einval.org/debian sid/main arm64 libpng16-16 arm64 1.6.37-3 [289 kB]
Get:110 http://mirror.einval.org/debian sid/main arm64 libfreetype6 arm64 2.10.4+dfsg-1 [393 kB]
Get:111 http://mirror.einval.org/debian sid/main arm64 libfontconfig1 arm64 2.13.1-4.2 [344 kB]
Get:112 http://mirror.einval.org/debian sid/main arm64 libidn11 arm64 1.33-3 [115 kB]
Get:113 http://mirror.einval.org/debian sid/main arm64 libijs-0.35 arm64 0.35-15 [15.8 kB]
Get:114 http://mirror.einval.org/debian sid/main arm64 libjbig2dec0 arm64 0.19-3 [62.8 kB]
Get:115 http://mirror.einval.org/debian sid/main arm64 libjpeg62-turbo arm64 1:2.0.6-4 [133 kB]
Get:116 http://mirror.einval.org/debian sid/main arm64 liblcms2-2 arm64 2.12~rc1-2 [140 kB]
Get:117 http://mirror.einval.org/debian sid/main arm64 libopenjp2-7 arm64 2.4.0-3 [160 kB]
Get:118 http://mirror.einval.org/debian sid/main arm64 libpaper1 arm64 1.1.28+b1 [21.4 kB]
Get:119 http://mirror.einval.org/debian sid/main arm64 libdeflate0 arm64 1.7-1 [47.7 kB]
Get:120 http://mirror.einval.org/debian sid/main arm64 libjbig0 arm64 2.1-3.1+b2 [27.8 kB]
Get:121 http://mirror.einval.org/debian sid/main arm64 libwebp6 arm64 0.6.1-2.1 [244 kB]
Get:122 http://mirror.einval.org/debian sid/main arm64 libtiff5 arm64 4.2.0-1 [276 kB]
Get:123 http://mirror.einval.org/debian sid/main arm64 libgs9 arm64 9.53.3~dfsg-7 [2071 kB]
Get:124 http://mirror.einval.org/debian sid/main arm64 ghostscript arm64 9.53.3~dfsg-7 [97.8 kB]
Get:125 http://mirror.einval.org/debian sid/main arm64 libnetpbm10 arm64 2:10.0-15.4 [83.9 kB]
Get:126 http://mirror.einval.org/debian sid/main arm64 netpbm arm64 2:10.0-15.4 [962 kB]
Get:127 http://mirror.einval.org/debian sid/main arm64 libpaper-utils arm64 1.1.28+b1 [18.3 kB]
Get:128 http://mirror.einval.org/debian sid/main arm64 libkpathsea6 arm64 2020.20200327.54578-7 [169 kB]
Get:129 http://mirror.einval.org/debian sid/main arm64 libptexenc1 arm64 2020.20200327.54578-7 [63.5 kB]
Get:130 http://mirror.einval.org/debian sid/main arm64 libsynctex2 arm64 2020.20200327.54578-7 [80.4 kB]
Get:131 http://mirror.einval.org/debian sid/main arm64 libtexlua53 arm64 2020.20200327.54578-7 [124 kB]
Get:132 http://mirror.einval.org/debian sid/main arm64 t1utils arm64 1.41-4 [59.8 kB]
Get:133 http://mirror.einval.org/debian sid/main arm64 libpixman-1-0 arm64 0.40.0-1 [444 kB]
Get:134 http://mirror.einval.org/debian sid/main arm64 libxau6 arm64 1:1.0.9-1 [19.7 kB]
Get:135 http://mirror.einval.org/debian sid/main arm64 libmd0 arm64 1.0.3-3 [27.9 kB]
Get:136 http://mirror.einval.org/debian sid/main arm64 libbsd0 arm64 0.11.3-1 [106 kB]
Get:137 http://mirror.einval.org/debian sid/main arm64 libxdmcp6 arm64 1:1.1.2-3 [25.4 kB]
Get:138 http://mirror.einval.org/debian sid/main arm64 libxcb1 arm64 1.14-3 [138 kB]
Get:139 http://mirror.einval.org/debian sid/main arm64 libx11-data all 2:1.7.1-1 [310 kB]
Get:140 http://mirror.einval.org/debian sid/main arm64 libx11-6 arm64 2:1.7.1-1 [747 kB]
Get:141 http://mirror.einval.org/debian sid/main arm64 libxcb-render0 arm64 1.14-3 [111 kB]
Get:142 http://mirror.einval.org/debian sid/main arm64 libxcb-shm0 arm64 1.14-3 [101 kB]
Get:143 http://mirror.einval.org/debian sid/main arm64 libxext6 arm64 2:1.3.3-1.1 [51.6 kB]
Get:144 http://mirror.einval.org/debian sid/main arm64 libxrender1 arm64 1:0.9.10-1 [30.4 kB]
Get:145 http://mirror.einval.org/debian sid/main arm64 libcairo2 arm64 1.16.0-5 [648 kB]
Get:146 http://mirror.einval.org/debian sid/main arm64 libgraphite2-3 arm64 1.3.14-1 [75.6 kB]
Get:147 http://mirror.einval.org/debian sid/main arm64 libglib2.0-0 arm64 2.66.8-1 [1286 kB]
Get:148 http://mirror.einval.org/debian sid/main arm64 libharfbuzz0b arm64 2.7.4-1 [1445 kB]
Get:149 http://mirror.einval.org/debian sid/main arm64 libteckit0 arm64 2.5.10+ds1-3 [293 kB]
Get:150 http://mirror.einval.org/debian sid/main arm64 x11-common all 1:7.7+22 [252 kB]
Get:151 http://mirror.einval.org/debian sid/main arm64 libice6 arm64 2:1.0.10-1 [55.6 kB]
Get:152 http://mirror.einval.org/debian sid/main arm64 libsm6 arm64 2:1.2.3-1 [34.0 kB]
Get:153 http://mirror.einval.org/debian sid/main arm64 libxt6 arm64 1:1.2.0-1 [176 kB]
Get:154 http://mirror.einval.org/debian sid/main arm64 libxmu6 arm64 2:1.1.2-2+b3 [57.8 kB]
Get:155 http://mirror.einval.org/debian sid/main arm64 libxpm4 arm64 1:3.5.12-1 [43.9 kB]
Get:156 http://mirror.einval.org/debian sid/main arm64 libxaw7 arm64 2:1.0.13-1.1 [184 kB]
Get:157 http://mirror.einval.org/debian sid/main arm64 libxi6 arm64 2:1.7.10-1 [81.7 kB]
Get:158 http://mirror.einval.org/debian sid/main arm64 libzzip-0-13 arm64 0.13.72+dfsg.1-1.1 [58.3 kB]
Get:159 http://mirror.einval.org/debian sid/main arm64 texlive-binaries arm64 2020.20200327.54578-7 [7572 kB]
Get:160 http://mirror.einval.org/debian sid/main arm64 xdg-utils all 1.1.3-4.1 [75.5 kB]
Get:161 http://mirror.einval.org/debian sid/main arm64 texlive-base all 2020.20210202-3 [20.8 MB]
Get:162 http://mirror.einval.org/debian sid/main arm64 hevea arm64 2.34-2+b1 [2015 kB]
Get:163 http://mirror.einval.org/debian sid/main amd64 libgcc-s1 amd64 10.2.1-6 [41.4 kB]
Get:164 http://mirror.einval.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.18-4 [87.5 kB]
Get:165 http://mirror.einval.org/debian sid/main amd64 libc6 amd64 2.31-13 [2811 kB]
Get:166 http://mirror.einval.org/debian sid/main amd64 libasan6 amd64 10.2.1-6 [2065 kB]
Get:167 http://mirror.einval.org/debian sid/main amd64 libatomic1 amd64 10.2.1-6 [9008 B]
Get:168 http://mirror.einval.org/debian sid/main amd64 libblkid1 amd64 2.36.1-7 [193 kB]
Get:169 http://mirror.einval.org/debian sid/main amd64 linux-libc-dev amd64 5.10.46-1 [1361 kB]
Get:170 http://mirror.einval.org/debian sid/main amd64 libcrypt-dev amd64 1:4.4.18-4 [104 kB]
Get:171 http://mirror.einval.org/debian sid/main amd64 libcom-err2 amd64 1.46.2-2 [74.2 kB]
Get:172 http://mirror.einval.org/debian sid/main amd64 libkrb5support0 amd64 1.18.3-5 [65.2 kB]
Get:173 http://mirror.einval.org/debian sid/main amd64 libk5crypto3 amd64 1.18.3-5 [114 kB]
Get:174 http://mirror.einval.org/debian sid/main amd64 libkeyutils1 amd64 1.6.1-2 [15.4 kB]
Get:175 http://mirror.einval.org/debian sid/main amd64 libssl1.1 amd64 1.1.1k-1 [1553 kB]
Get:176 http://mirror.einval.org/debian sid/main amd64 libkrb5-3 amd64 1.18.3-5 [363 kB]
Get:177 http://mirror.einval.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.18.3-5 [165 kB]
Get:178 http://mirror.einval.org/debian sid/main amd64 libtirpc3 amd64 1.3.1-1 [83.6 kB]
Get:179 http://mirror.einval.org/debian sid/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB]
Get:180 http://mirror.einval.org/debian sid/main amd64 libtirpc-dev amd64 1.3.1-1 [190 kB]
Get:181 http://mirror.einval.org/debian sid/main amd64 libnsl-dev amd64 1.3.0-2 [66.4 kB]
Get:182 http://mirror.einval.org/debian sid/main amd64 libc6-dev amd64 2.31-13 [2344 kB]
Get:183 http://mirror.einval.org/debian sid/main amd64 libuuid1 amd64 2.36.1-7 [83.6 kB]
Get:184 http://mirror.einval.org/debian sid/main amd64 uuid-dev amd64 2.36.1-7 [99.2 kB]
Get:185 http://mirror.einval.org/debian sid/main amd64 libblkid-dev amd64 2.36.1-7 [224 kB]
Get:186 http://mirror.einval.org/debian sid/main arm64 libdatrie1 arm64 0.2.13-1 [42.1 kB]
Get:187 http://mirror.einval.org/debian sid/main amd64 libffi7 amd64 3.3-6 [23.1 kB]
Get:188 http://mirror.einval.org/debian sid/main amd64 libffi-dev amd64 3.3-6 [56.5 kB]
Get:189 http://mirror.einval.org/debian sid/main arm64 libfontenc1 arm64 1:1.1.4-1 [23.6 kB]
Get:190 http://mirror.einval.org/debian sid/main amd64 libgomp1 amd64 10.2.1-6 [99.9 kB]
Get:191 http://mirror.einval.org/debian sid/main amd64 libitm1 amd64 10.2.1-6 [25.8 kB]
Get:192 http://mirror.einval.org/debian sid/main amd64 liblsan0 amd64 10.2.1-6 [828 kB]
Get:193 http://mirror.einval.org/debian sid/main amd64 libtsan0 amd64 10.2.1-6 [2000 kB]
Get:194 http://mirror.einval.org/debian sid/main amd64 libstdc++6 amd64 10.2.1-6 [493 kB]
Get:195 http://mirror.einval.org/debian sid/main amd64 libubsan1 amd64 10.2.1-6 [777 kB]
Get:196 http://mirror.einval.org/debian sid/main amd64 libquadmath0 amd64 10.2.1-6 [145 kB]
Get:197 http://mirror.einval.org/debian sid/main amd64 libgcc-10-dev amd64 10.2.1-6 [2328 kB]
Get:198 http://mirror.einval.org/debian sid/main amd64 libpcre2-8-0 amd64 10.36-2 [247 kB]
Get:199 http://mirror.einval.org/debian sid/main amd64 libselinux1 amd64 3.1-3 [88.1 kB]
Get:200 http://mirror.einval.org/debian sid/main amd64 libmount1 amd64 2.36.1-7 [211 kB]
Get:201 http://mirror.einval.org/debian sid/main amd64 libpcre3 amd64 2:8.39-13 [343 kB]
Get:202 http://mirror.einval.org/debian sid/main amd64 zlib1g amd64 1:1.2.11.dfsg-2 [90.4 kB]
Get:203 http://mirror.einval.org/debian sid/main amd64 libglib2.0-0 amd64 2.66.8-1 [1370 kB]
Get:204 http://mirror.einval.org/debian sid/main arm64 libglib2.0-data all 2.66.8-1 [1164 kB]
Get:205 http://mirror.einval.org/debian sid/main arm64 libglib2.0-bin arm64 2.66.8-1 [137 kB]
Get:206 http://mirror.einval.org/debian sid/main arm64 python3-lib2to3 all 3.9.2-1 [77.8 kB]
Get:207 http://mirror.einval.org/debian sid/main arm64 python3-distutils all 3.9.2-1 [143 kB]
Get:208 http://mirror.einval.org/debian sid/main arm64 libglib2.0-dev-bin arm64 2.66.8-1 [177 kB]
Get:209 http://mirror.einval.org/debian sid/main amd64 libsepol1 amd64 3.1-1 [265 kB]
Get:210 http://mirror.einval.org/debian sid/main amd64 libsepol1-dev amd64 3.1-1 [338 kB]
Get:211 http://mirror.einval.org/debian sid/main amd64 libpcre2-16-0 amd64 10.36-2 [231 kB]
Get:212 http://mirror.einval.org/debian sid/main amd64 libpcre2-32-0 amd64 10.36-2 [220 kB]
Get:213 http://mirror.einval.org/debian sid/main amd64 libpcre2-posix2 amd64 10.36-2 [49.1 kB]
Get:214 http://mirror.einval.org/debian sid/main amd64 libpcre2-dev amd64 10.36-2 [731 kB]
Get:215 http://mirror.einval.org/debian sid/main amd64 libselinux1-dev amd64 3.1-3 [168 kB]
Get:216 http://mirror.einval.org/debian sid/main amd64 libmount-dev amd64 2.36.1-7 [77.8 kB]
Get:217 http://mirror.einval.org/debian sid/main amd64 libpcre16-3 amd64 2:8.39-13 [259 kB]
Get:218 http://mirror.einval.org/debian sid/main amd64 libpcre32-3 amd64 2:8.39-13 [250 kB]
Get:219 http://mirror.einval.org/debian sid/main amd64 libpcrecpp0v5 amd64 2:8.39-13 [152 kB]
Get:220 http://mirror.einval.org/debian sid/main amd64 libpcre3-dev amd64 2:8.39-13 [650 kB]
Get:221 http://mirror.einval.org/debian sid/main arm64 pkg-config arm64 0.29.2-1 [63.6 kB]
Get:222 http://mirror.einval.org/debian sid/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB]
Get:223 http://mirror.einval.org/debian sid/main amd64 libglib2.0-dev amd64 2.66.8-1 [1577 kB]
Get:224 http://mirror.einval.org/debian sid/main arm64 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB]
Get:225 http://mirror.einval.org/debian sid/main arm64 libmime-charset-perl all 1.012.2-1 [35.4 kB]
Get:226 http://mirror.einval.org/debian sid/main arm64 libthai-data all 0.1.28-4 [171 kB]
Get:227 http://mirror.einval.org/debian sid/main arm64 libthai0 arm64 0.1.28-4 [53.1 kB]
Get:228 http://mirror.einval.org/debian sid/main arm64 libsombok3 arm64 2.4.0-2+b1 [29.8 kB]
Get:229 http://mirror.einval.org/debian sid/main amd64 libstdc++-10-dev amd64 10.2.1-6 [1741 kB]
Get:230 http://mirror.einval.org/debian sid/main arm64 libunicode-linebreak-perl arm64 0.0.20190101-1+b2 [101 kB]
Get:231 http://mirror.einval.org/debian sid/main arm64 xfonts-encodings all 1:1.0.4-2.1 [573 kB]
Get:232 http://mirror.einval.org/debian sid/main arm64 xfonts-utils arm64 1:7.7+6 [85.6 kB]
Get:233 http://mirror.einval.org/debian sid/main arm64 lmodern all 2.004.5-6.1 [9489 kB]
Get:234 http://mirror.einval.org/debian sid/main arm64 texlive-latex-base all 2020.20210202-3 [1120 kB]
Get:235 http://mirror.einval.org/debian sid/main arm64 texlive-luatex all 2020.20210202-3 [14.4 MB]
Get:236 http://mirror.einval.org/debian sid/main arm64 texlive-plain-generic all 2020.20210202-3 [27.0 MB]
Get:237 http://mirror.einval.org/debian sid/main arm64 texlive-extra-utils all 2020.20210202-3 [55.5 MB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 391 MB in 7s (54.6 MB/s)
Selecting previously unselected package bsdextrautils.
(Reading database ... 12271 files and directories currently installed.)
Preparing to unpack .../0-bsdextrautils_2.36.1-7_arm64.deb ...
Unpacking bsdextrautils (2.36.1-7) ...
Selecting previously unselected package libuchardet0:arm64.
Preparing to unpack .../1-libuchardet0_0.0.7-1_arm64.deb ...
Unpacking libuchardet0:arm64 (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../2-groff-base_1.22.4-6_arm64.deb ...
Unpacking groff-base (1.22.4-6) ...
Selecting previously unselected package libpipeline1:arm64.
Preparing to unpack .../3-libpipeline1_1.5.3-1_arm64.deb ...
Unpacking libpipeline1:arm64 (1.5.3-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../4-man-db_2.9.4-2_arm64.deb ...
Unpacking man-db (2.9.4-2) ...
Selecting previously unselected package liblocale-gettext-perl.
Preparing to unpack .../5-liblocale-gettext-perl_1.07-4+b1_arm64.deb ...
Unpacking liblocale-gettext-perl (1.07-4+b1) ...
Selecting previously unselected package poppler-data.
Preparing to unpack .../6-poppler-data_0.4.10-1_all.deb ...
Unpacking poppler-data (0.4.10-1) ...
Selecting previously unselected package libpython3.9-minimal:arm64.
Preparing to unpack .../7-libpython3.9-minimal_3.9.2-1_arm64.deb ...
Unpacking libpython3.9-minimal:arm64 (3.9.2-1) ...
Selecting previously unselected package libexpat1:arm64.
Preparing to unpack .../8-libexpat1_2.2.10-2_arm64.deb ...
Unpacking libexpat1:arm64 (2.2.10-2) ...
Selecting previously unselected package python3.9-minimal.
Preparing to unpack .../9-python3.9-minimal_3.9.2-1_arm64.deb ...
Unpacking python3.9-minimal (3.9.2-1) ...
Setting up libpython3.9-minimal:arm64 (3.9.2-1) ...
Setting up libexpat1:arm64 (2.2.10-2) ...
Setting up python3.9-minimal (3.9.2-1) ...
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Setting up fonts-urw-base35 (20200910-1) ...
Setting up libyaml-perl (1.30-1) ...
Setting up libjbig0:arm64 (2.1-3.1+b2) ...
Setting up poppler-data (0.4.10-1) ...
Setting up libosp5 (1.5.2-13+b2) ...
Setting up libxml-sax-base-perl (1.09-1.1) ...
Setting up libio-string-perl (1.08-3.1) ...
Setting up gcc-10-base:amd64 (10.2.1-6) ...
Setting up libfontenc1:arm64 (1:1.1.4-1) ...
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up libglib2.0-data (2.66.8-1) ...
Setting up cross-config (2.6.18+nmu1) ...
Setting up libjpeg62-turbo:arm64 (1:2.0.6-4) ...
Setting up libx11-data (2:1.7.1-1) ...
Setting up libjbig2dec0:arm64 (0.19-3) ...
Setting up libidn11:arm64 (1.33-3) ...
Setting up libteckit0:arm64 (2.5.10+ds1-3) ...
Setting up libavahi-common-data:arm64 (0.8-5) ...
Setting up libdbus-1-3:arm64 (1.12.20-2) ...
Setting up libsigsegv2:arm64 (2.13-1) ...
Setting up xfonts-encodings (1:1.0.4-2.1) ...
Setting up t1utils (1.41-4) ...
Setting up libpng16-16:arm64 (1.6.37-3) ...
Setting up autopoint (0.21-4) ...
Setting up libwebp6:arm64 (0.6.1-2.1) ...
Setting up pkg-config (0.29.2-1) ...
Setting up fonts-dejavu-core (2.37-2) ...
Setting up libc6-amd64-cross (2.31-9cross4) ...
Setting up libncursesw6:arm64 (6.2+20201114-2) ...
Setting up gcc-10-cross-base (10.2.1-6cross1) ...
Setting up libkpathsea6:arm64 (2020.20200327.54578-7) ...
Setting up libmd0:arm64 (1.0.3-3) ...
Setting up sensible-utils (0.0.14) ...
Setting up libmime-charset-perl (1.012.2-1) ...
Setting up libuchardet0:arm64 (0.0.7-1) ...
Setting up gcc-10-x86-64-linux-gnu-base:arm64 (10.2.1-6cross1) ...
Setting up libmpdec3:arm64 (2.5.1-2) ...
Setting up fonts-lmodern (2.004.5-6.1) ...
Setting up libopenjp2-7:arm64 (2.4.0-3) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libthai-data (0.1.28-4) ...
Setting up sgml-base (1.30) ...
Setting up libtiff5:arm64 (4.2.0-1) ...
Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ...
Setting up libgcc-s1-amd64-cross (10.2.1-6cross1) ...
Setting up libfile-homedir-perl (1.006-1) ...
Setting up libbsd0:arm64 (0.11.3-1) ...
Setting up libelf1:arm64 (0.183-3) ...
Setting up readline-common (8.1-2) ...
Setting up libxml2:arm64 (2.9.10+dfsg-6.7) ...
Setting up xdg-utils (1.1.3-4.1) ...
update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
Setting up liblocale-gettext-perl (1.07-4+b1) ...
Setting up libasan6-amd64-cross (10.2.1-6cross1) ...
Setting up libsynctex2:arm64 (2020.20200327.54578-7) ...
Setting up binutils-x86-64-linux-gnu (2.35.2-2) ...
Setting up libstdc++6-amd64-cross (10.2.1-6cross1) ...
Setting up libgs9-common (9.53.3~dfsg-7) ...
Setting up libfile-stripnondeterminism-perl (1.12.0-1) ...
Setting up libice6:arm64 (2:1.0.10-1) ...
Setting up libxdmcp6:arm64 (1:1.1.2-3) ...
Setting up libxcb1:arm64 (1.14-3) ...
Setting up gettext (0.21-4) ...
Setting up libtool (2.4.6-15) ...
Setting up libxcb-render0:arm64 (1.14-3) ...
Setting up liblsan0-amd64-cross (10.2.1-6cross1) ...
Setting up libc6-dev-amd64-cross (2.31-9cross4) ...
Setting up libreadline8:arm64 (8.1-2) ...
Setting up libtsan0-amd64-cross (10.2.1-6cross1) ...
Setting up libavahi-common3:arm64 (0.8-5) ...
Setting up libglib2.0-bin (2.66.8-1) ...
Setting up cpp-10-x86-64-linux-gnu (10.2.1-6cross1) ...
Setting up m4 (1.4.18-5) ...
Setting up libxcb-shm0:arm64 (1.14-3) ...
Setting up opensp (1.5.2-13+b2) ...
Setting up libgomp1-amd64-cross (10.2.1-6cross1) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libitm1-amd64-cross (10.2.1-6cross1) ...
Setting up libthai0:arm64 (0.1.28-4) ...
Setting up libptexenc1:arm64 (2020.20200327.54578-7) ...
Setting up libatomic1-amd64-cross (10.2.1-6cross1) ...
Setting up libfreetype6:arm64 (2.10.4+dfsg-1) ...
Setting up libquadmath0-amd64-cross (10.2.1-6cross1) ...
Setting up libubsan1-amd64-cross (10.2.1-6cross1) ...
Setting up ucf (3.0043) ...
Setting up netpbm (2:10.0-15.4) ...
Setting up autoconf (2.69-14) ...
Setting up dh-strip-nondeterminism (1.12.0-1) ...
Setting up dwz (0.14-1) ...
Setting up groff-base (1.22.4-6) ...
Setting up xml-core (0.18+nmu1) ...
Setting up libx11-6:arm64 (2:1.7.1-1) ...
Setting up libharfbuzz0b:arm64 (2.7.4-1) ...
Setting up libsm6:arm64 (2:1.2.3-1) ...
Setting up libavahi-client3:arm64 (0.8-5) ...
Setting up libpython3.9-stdlib:arm64 (3.9.2-1) ...
Setting up libpython3-stdlib:arm64 (3.9.2-3) ...
Setting up cpp-x86-64-linux-gnu (4:10.2.1-1) ...
Setting up automake (1:1.16.3-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libpaper1:arm64 (1.1.28+b1) ...

Creating config file /etc/papersize with new version
Setting up libxpm4:arm64 (1:3.5.12-1) ...
Setting up libxrender1:arm64 (1:0.9.10-1) ...
Setting up libsombok3:arm64 (2.4.0-2+b1) ...
Setting up fontconfig-config (2.13.1-4.2) ...
Setting up libgcc-10-dev-amd64-cross (10.2.1-6cross1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libxext6:arm64 (2:1.3.3-1.1) ...
Setting up libpaper-utils (1.1.28+b1) ...
Setting up xfonts-utils (1:7.7+6) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libxml-sax-perl (1.02+dfsg-1) ...
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 dh-autoreconf (20) ...
Setting up tex-common (6.16) ...
update-language: texlive-base not installed and configured, doing nothing!
Setting up libunicode-linebreak-perl (0.0.20190101-1+b2) ...
Setting up libxt6:arm64 (1:1.2.0-1) ...
Setting up libxml-libxml-perl (2.0134+dfsg-2+b1) ...
update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50...
update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50...
update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...
Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version
Setting up libcups2:arm64 (2.3.3op2-3+deb11u1) ...
Setting up lmodern (2.004.5-6.1) ...
Setting up libfontconfig1:arm64 (2.13.1-4.2) ...
Setting up gcc-10-x86-64-linux-gnu (10.2.1-6cross1) ...
Setting up python3.9 (3.9.2-1) ...
Setting up libxmu6:arm64 (2:1.1.2-2+b3) ...
Setting up libgs9:arm64 (9.53.3~dfsg-7) ...
Setting up libstdc++-10-dev-amd64-cross (10.2.1-6cross1) ...
Setting up libxi6:arm64 (2:1.7.10-1) ...
Setting up gcc-x86-64-linux-gnu (4:10.2.1-1) ...
Setting up debhelper (13.3.4) ...
Setting up python3 (3.9.2-3) ...
Setting up libxaw7:arm64 (2:1.0.13-1.1) ...
Setting up ghostscript (9.53.3~dfsg-7) ...
Setting up g++-10-x86-64-linux-gnu (10.2.1-6cross1) ...
Setting up libcairo2:arm64 (1.16.0-5) ...
Setting up libxml-simple-perl (2.25-1) ...
Setting up texlive-binaries (2020.20200327.54578-7) ...
update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode
update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode
Setting up g++-x86-64-linux-gnu (4:10.2.1-1) ...
Setting up python3-lib2to3 (3.9.2-1) ...
Setting up texlive-base (2020.20210202-3) ...
tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps
tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg
tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper
tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex
Setting up python3-distutils (3.9.2-1) ...
Setting up libglib2.0-dev-bin (2.66.8-1) ...
Setting up texlive-luatex (2020.20210202-3) ...
Setting up texlive-plain-generic (2020.20210202-3) ...
Setting up libconfig-auto-perl (0.44-1.1) ...
Setting up texlive-latex-base (2020.20210202-3) ...
Setting up texlive-extra-utils (2020.20210202-3) ...
Setting up hevea (2.34-2+b1) ...
Setting up libdebian-dpkgcross-perl (2.6.18+nmu1) ...
Setting up dpkg-cross (2.6.18+nmu1) ...
Setting up crossbuild-essential-amd64 (12.9) ...
Setting up libcrypt1:amd64 (1:4.4.18-4) ...
Setting up libgcc-s1:amd64 (10.2.1-6) ...
Setting up libc6:amd64 (2.31-13) ...
Setting up libsepol1:amd64 (3.1-1) ...
Setting up libcrypt-dev:amd64 (1:4.4.18-4) ...
Setting up libblkid1:amd64 (2.36.1-7) ...
Setting up libstdc++6:amd64 (10.2.1-6) ...
Setting up liblsan0:amd64 (10.2.1-6) ...
Setting up libitm1:amd64 (10.2.1-6) ...
Setting up libtsan0:amd64 (10.2.1-6) ...
Setting up libkeyutils1:amd64 (1.6.1-2) ...
Setting up libpcre16-3:amd64 (2:8.39-13) ...
Setting up libssl1.1:amd64 (1.1.1k-1) ...
Setting up libffi7:amd64 (3.3-6) ...
Setting up libsepol1-dev:amd64 (3.1-1) ...
Setting up zlib1g:amd64 (1:1.2.11.dfsg-2) ...
Setting up libcom-err2:amd64 (1.46.2-2) ...
Setting up libgomp1:amd64 (10.2.1-6) ...
Setting up libffi-dev:amd64 (3.3-6) ...
Setting up libpcre2-16-0:amd64 (10.36-2) ...
Setting up libasan6:amd64 (10.2.1-6) ...
Setting up libkrb5support0:amd64 (1.18.3-5) ...
Setting up libpcre3:amd64 (2:8.39-13) ...
Setting up libpcre2-32-0:amd64 (10.36-2) ...
Setting up libquadmath0:amd64 (10.2.1-6) ...
Setting up libpcre32-3:amd64 (2:8.39-13) ...
Setting up libatomic1:amd64 (10.2.1-6) ...
Setting up libuuid1:amd64 (2.36.1-7) ...
Setting up libpcre2-8-0:amd64 (10.36-2) ...
Setting up libk5crypto3:amd64 (1.18.3-5) ...
Setting up libubsan1:amd64 (10.2.1-6) ...
Setting up libkrb5-3:amd64 (1.18.3-5) ...
Setting up libpcrecpp0v5:amd64 (2:8.39-13) ...
Setting up libgcc-10-dev:amd64 (10.2.1-6) ...
Setting up libselinux1:amd64 (3.1-3) ...
Setting up libgssapi-krb5-2:amd64 (1.18.3-5) ...
Setting up libpcre2-posix2:amd64 (10.36-2) ...
Setting up libmount1:amd64 (2.36.1-7) ...
Setting up libtirpc3:amd64 (1.3.1-1) ...
Setting up libglib2.0-0:amd64 (2.66.8-1) ...
/var/lib/dpkg/info/libglib2.0-0:amd64.postinst: 62: /usr/lib/x86_64-linux-gnu/glib-2.0/glib-compile-schemas: Exec format error
/var/lib/dpkg/info/libglib2.0-0:amd64.postinst: 65: /usr/lib/x86_64-linux-gnu/glib-2.0/gio-querymodules: Exec format error
Setting up libtirpc-dev:amd64 (1.3.1-1) ...
Setting up libnsl2:amd64 (1.3.0-2) ...
Setting up libnsl-dev:amd64 (1.3.0-2) ...
Setting up libc6-dev:amd64 (2.31-13) ...
Setting up libstdc++-10-dev:amd64 (10.2.1-6) ...
Setting up libpcre2-dev:amd64 (10.36-2) ...
Setting up libselinux1-dev:amd64 (3.1-3) ...
Setting up libpcre3-dev:amd64 (2:8.39-13) ...
Setting up uuid-dev:amd64 (2.36.1-7) ...
Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2) ...
Setting up libblkid-dev:amd64 (2.36.1-7) ...
Setting up libmount-dev:amd64 (2.36.1-7) ...
Setting up libglib2.0-dev:amd64 (2.66.8-1) ...
Processing triggers for libc-bin (2.31-13) ...
Processing triggers for sgml-base (1.30) ...
Setting up sgml-data (2.0.11+nmu1) ...
Processing triggers for sgml-base (1.30) ...
Setting up docbook (4.5-6) ...
Processing triggers for sgml-base (1.30) ...
Setting up docbook-to-man (1:2.0.0-45) ...
Setting up sbuild-build-depends-main-dummy:amd64 (0.invalid.0) ...
Processing triggers for tex-common (6.16) ...
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 (amd64 included in any all)

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 5.9.0-0.bpo.2-arm64 #1 SMP Debian 5.9.6-1~bpo10+1 (2020-11-19) arm64 (aarch64)
Toolchain package versions: binutils_2.35.2-2 dpkg-dev_1.20.9 g++-10_10.2.1-6 gcc-10_10.2.1-6 libc6-dev_2.31-13 libstdc++-10-dev_10.2.1-6 libstdc++-10-dev-amd64-cross_10.2.1-6cross1 libstdc++6_10.2.1-6 libstdc++6-amd64-cross_10.2.1-6cross1 linux-libc-dev_5.10.46-1
Package versions: adduser_3.118 apt_2.2.4 autoconf_2.69-14 automake_1:1.16.3-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_11.1 base-passwd_3.5.51 bash_5.1-3 binutils_2.35.2-2 binutils-aarch64-linux-gnu_2.35.2-2 binutils-common_2.35.2-2 binutils-x86-64-linux-gnu_2.35.2-2 bsdextrautils_2.36.1-7 bsdutils_1:2.36.1-7 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.1-1 cpp-10_10.2.1-6 cpp-10-x86-64-linux-gnu_10.2.1-6cross1 cpp-x86-64-linux-gnu_4:10.2.1-1 cross-config_2.6.18+nmu1 crossbuild-essential-amd64_12.9 dash_0.5.11+git20210120+802ebd4-1 debconf_1.5.77 debhelper_13.3.4 debian-archive-keyring_2021.1.1 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-1 diffutils_1:3.7-5 docbook_4.5-6 docbook-to-man_1:2.0.0-45 dpkg_1.20.9 dpkg-cross_2.6.18+nmu1 dpkg-dev_1.20.9 dwz_0.14-1 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 fontconfig-config_2.13.1-4.2 fonts-dejavu-core_2.37-2 fonts-lmodern_2.004.5-6.1 fonts-urw-base35_20200910-1 g++_4:10.2.1-1 g++-10_10.2.1-6 g++-10-x86-64-linux-gnu_10.2.1-6cross1 g++-x86-64-linux-gnu_4:10.2.1-1 gcc_4:10.2.1-1 gcc-10_10.2.1-6 gcc-10-base_10.2.1-6 gcc-10-cross-base_10.2.1-6cross1 gcc-10-x86-64-linux-gnu_10.2.1-6cross1 gcc-10-x86-64-linux-gnu-base_10.2.1-6cross1 gcc-x86-64-linux-gnu_4:10.2.1-1 gettext_0.21-4 gettext-base_0.21-4 ghostscript_9.53.3~dfsg-7 gpgv_2.2.27-2 grep_3.6-1 groff-base_1.22.4-6 gzip_1.10-4 hevea_2.34-2+b1 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-10 libapt-pkg6.0_2.2.4 libarchive-zip-perl_1.68-1 libasan6_10.2.1-6 libasan6-amd64-cross_10.2.1-6cross1 libatomic1_10.2.1-6 libatomic1-amd64-cross_10.2.1-6cross1 libattr1_1:2.4.48-6 libaudit-common_1:3.0-2 libaudit1_1:3.0-2 libavahi-client3_0.8-5 libavahi-common-data_0.8-5 libavahi-common3_0.8-5 libbinutils_2.35.2-2 libblkid-dev_2.36.1-7 libblkid1_2.36.1-7 libbrotli1_1.0.9-2+b2 libbsd0_0.11.3-1 libbz2-1.0_1.0.8-4 libc-bin_2.31-13 libc-dev-bin_2.31-13 libc6_2.31-13 libc6-amd64-cross_2.31-9cross4 libc6-dev_2.31-13 libc6-dev-amd64-cross_2.31-9cross4 libcairo2_1.16.0-5 libcap-ng0_0.7.9-2.2+b1 libcc1-0_10.2.1-6 libcom-err2_1.46.2-2 libconfig-auto-perl_0.44-1.1 libconfig-inifiles-perl_3.000003-1 libcrypt-dev_1:4.4.18-4 libcrypt1_1:4.4.18-4 libctf-nobfd0_2.35.2-2 libctf0_2.35.2-2 libcups2_2.3.3op2-3+deb11u1 libdatrie1_0.2.13-1 libdb5.3_5.3.28+dfsg1-0.8 libdbus-1-3_1.12.20-2 libdebconfclient0_0.260 libdebhelper-perl_13.3.4 libdebian-dpkgcross-perl_2.6.18+nmu1 libdeflate0_1.7-1 libdpkg-perl_1.20.9 libelf1_0.183-3 libexpat1_2.2.10-2 libfakeroot_1.25.3-1.1 libffi-dev_3.3-6 libffi7_3.3-6 libfile-homedir-perl_1.006-1 libfile-stripnondeterminism-perl_1.12.0-1 libfile-which-perl_1.23-1 libfontconfig1_2.13.1-4.2 libfontenc1_1:1.1.4-1 libfreetype6_2.10.4+dfsg-1 libgcc-10-dev_10.2.1-6 libgcc-10-dev-amd64-cross_10.2.1-6cross1 libgcc-s1_10.2.1-6 libgcc-s1-amd64-cross_10.2.1-6cross1 libgcrypt20_1.8.7-6 libgdbm-compat4_1.19-2 libgdbm6_1.19-2 libglib2.0-0_2.66.8-1 libglib2.0-bin_2.66.8-1 libglib2.0-data_2.66.8-1 libglib2.0-dev_2.66.8-1 libglib2.0-dev-bin_2.66.8-1 libgmp10_2:6.2.1+dfsg-1 libgnutls30_3.7.1-5 libgomp1_10.2.1-6 libgomp1-amd64-cross_10.2.1-6cross1 libgpg-error0_1.38-2 libgraphite2-3_1.3.14-1 libgs9_9.53.3~dfsg-7 libgs9-common_9.53.3~dfsg-7 libgssapi-krb5-2_1.18.3-5 libharfbuzz0b_2.7.4-1 libhogweed6_3.7.3-1 libice6_2:1.0.10-1 libicu67_67.1-7 libidn11_1.33-3 libidn2-0_2.3.0-5 libijs-0.35_0.35-15 libio-string-perl_1.08-3.1 libisl23_0.23-1 libitm1_10.2.1-6 libitm1-amd64-cross_10.2.1-6cross1 libjbig0_2.1-3.1+b2 libjbig2dec0_0.19-3 libjpeg62-turbo_1:2.0.6-4 libjs-jquery_3.5.1+dfsg+~3.5.5-7 libk5crypto3_1.18.3-5 libkeyutils1_1.6.1-2 libkpathsea6_2020.20200327.54578-7 libkrb5-3_1.18.3-5 libkrb5support0_1.18.3-5 liblcms2-2_2.12~rc1-2 liblocale-gettext-perl_1.07-4+b1 liblsan0_10.2.1-6 liblsan0-amd64-cross_10.2.1-6cross1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmd0_1.0.3-3 libmime-charset-perl_1.012.2-1 libmount-dev_2.36.1-7 libmount1_2.36.1-7 libmpc3_1.2.0-1 libmpdec3_2.5.1-2 libmpfr6_4.1.0-3 libncursesw6_6.2+20201114-2 libnetpbm10_2:10.0-15.4 libnettle8_3.7.3-1 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libopenjp2-7_2.4.0-3 libosp5_1.5.2-13+b2 libp11-kit0_0.23.22-1 libpam-modules_1.4.0-9 libpam-modules-bin_1.4.0-9 libpam-runtime_1.4.0-9 libpam0g_1.4.0-9 libpaper-utils_1.1.28+b1 libpaper1_1.1.28+b1 libpcre16-3_2:8.39-13 libpcre2-16-0_10.36-2 libpcre2-32-0_10.36-2 libpcre2-8-0_10.36-2 libpcre2-dev_10.36-2 libpcre2-posix2_10.36-2 libpcre3_2:8.39-13 libpcre3-dev_2:8.39-13 libpcre32-3_2:8.39-13 libpcrecpp0v5_2:8.39-13 libperl5.32_5.32.1-4 libpipeline1_1.5.3-1 libpixman-1-0_0.40.0-1 libpng16-16_1.6.37-3 libptexenc1_2020.20200327.54578-7 libpython3-stdlib_3.9.2-3 libpython3.9-minimal_3.9.2-1 libpython3.9-stdlib_3.9.2-1 libquadmath0_10.2.1-6 libquadmath0-amd64-cross_10.2.1-6cross1 libreadline8_8.1-2 libseccomp2_2.5.1-1 libselinux1_3.1-3 libselinux1-dev_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b2 libsepol1_3.1-1 libsepol1-dev_3.1-1 libsigsegv2_2.13-1 libsm6_2:1.2.3-1 libsmartcols1_2.36.1-7 libsombok3_2.4.0-2+b1 libsqlite3-0_3.34.1-3 libssl1.1_1.1.1k-1 libstdc++-10-dev_10.2.1-6 libstdc++-10-dev-amd64-cross_10.2.1-6cross1 libstdc++6_10.2.1-6 libstdc++6-amd64-cross_10.2.1-6cross1 libsub-override-perl_0.09-2 libsynctex2_2020.20200327.54578-7 libsystemd0_247.3-5 libtasn1-6_4.16.0-2 libteckit0_2.5.10+ds1-3 libtexlua53_2020.20200327.54578-7 libthai-data_0.1.28-4 libthai0_0.1.28-4 libtiff5_4.2.0-1 libtinfo6_6.2+20201114-2 libtirpc-common_1.3.1-1 libtirpc-dev_1.3.1-1 libtirpc3_1.3.1-1 libtool_2.4.6-15 libtsan0_10.2.1-6 libtsan0-amd64-cross_10.2.1-6cross1 libubsan1_10.2.1-6 libubsan1-amd64-cross_10.2.1-6cross1 libuchardet0_0.0.7-1 libudev1_247.3-5 libunicode-linebreak-perl_0.0.20190101-1+b2 libunistring2_0.9.10-4 libuuid1_2.36.1-7 libwebp6_0.6.1-2.1 libx11-6_2:1.7.1-1 libx11-data_2:1.7.1-1 libxau6_1:1.0.9-1 libxaw7_2:1.0.13-1.1 libxcb-render0_1.14-3 libxcb-shm0_1.14-3 libxcb1_1.14-3 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1.1 libxi6_2:1.7.10-1 libxml-libxml-perl_2.0134+dfsg-2+b1 libxml-namespacesupport-perl_1.12-1.1 libxml-sax-base-perl_1.09-1.1 libxml-sax-perl_1.02+dfsg-1 libxml-simple-perl_2.25-1 libxml2_2.9.10+dfsg-6.7 libxmu6_2:1.1.2-2+b3 libxpm4_1:3.5.12-1 libxrender1_1:0.9.10-1 libxt6_1:1.2.0-1 libxxhash0_0.8.0-2 libyaml-perl_1.30-1 libzstd1_1.4.8+dfsg-2.1 libzzip-0-13_0.13.72+dfsg.1-1.1 linux-libc-dev_5.10.46-1 linux-libc-dev-amd64-cross_5.10.13-1cross4 lmodern_2.004.5-6.1 login_1:4.8.1-1 lsb-base_11.1.0 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 media-types_4.0.0 mount_2.36.1-7 ncurses-base_6.2+20201114-2 ncurses-bin_6.2+20201114-2 netpbm_2:10.0-15.4 opensp_1.5.2-13+b2 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-4 perl-base_5.32.1-4 perl-modules-5.32_5.32.1-4 pkg-config_0.29.2-1 po-debconf_1.0.21+nmu1 poppler-data_0.4.10-1 python3_3.9.2-3 python3-distutils_3.9.2-1 python3-lib2to3_3.9.2-1 python3-minimal_3.9.2-3 python3.9_3.9.2-1 python3.9-minimal_3.9.2-1 readline-common_8.1-2 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.14 sgml-base_1.30 sgml-data_2.0.11+nmu1 sysvinit-utils_2.96-7 t1utils_1.41-4 tar_1.34+dfsg-1 tex-common_6.16 texlive-base_2020.20210202-3 texlive-binaries_2020.20200327.54578-7 texlive-extra-utils_2020.20210202-3 texlive-latex-base_2020.20210202-3 texlive-luatex_2020.20210202-3 texlive-plain-generic_2020.20210202-3 tzdata_2021a-1 ucf_3.0043 util-linux_2.36.1-7 uuid-dev_2.36.1-7 x11-common_1:7.7+22 xdg-utils_1.1.3-4.1 xfonts-encodings_1:1.0.4-2.1 xfonts-utils_1:7.7+6 xml-core_0.18+nmu1 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 3.0 (quilt)
Source: wise
Binary: wise, wise-doc, wise-data
Architecture: any all
Version: 2.4.1-23
Maintainer: Debian Med Packaging Team <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: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/wise
Vcs-Git: https://salsa.debian.org/med-team/wise.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 12), texlive-latex-base, texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev
Package-List:
 wise deb science optional arch=any
 wise-data deb doc optional arch=all
 wise-doc deb doc optional arch=all
Checksums-Sha1:
 50215e0541ed043d2ee44463da1b1a0d5272d724 3410178 wise_2.4.1.orig.tar.gz
 3a0b88d342fb1b6ac2ee20ced2dcbcdf44795439 27152 wise_2.4.1-23.debian.tar.xz
Checksums-Sha256:
 0aec5e30739110783517a429606249fc6c5fd0d65171c1a6d79ecc5ff81d2935 3410178 wise_2.4.1.orig.tar.gz
 432297bafe4688cd3f3041e5d8897792ef1b7cd3afb7bef3d06274abf28d7772 27152 wise_2.4.1-23.debian.tar.xz
Files:
 9e90132c19a653831ce63b5af7f08302 3410178 wise_2.4.1.orig.tar.gz
 55b2719ab85acb83f518de3c19708e95 27152 wise_2.4.1-23.debian.tar.xz

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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.8LbWx2Kr/trustedkeys.kbx': General error
gpgv: Signature made Sat Apr 18 16:13:39 2020 UTC
gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv:                issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./wise_2.4.1-23.dsc
dpkg-source: info: extracting wise in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking wise_2.4.1.orig.tar.gz
dpkg-source: info: unpacking wise_2.4.1-23.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying 01_welcome-csh.patch
dpkg-source: info: applying 02_isnumber.patch
dpkg-source: info: applying 03_doc-nodycache.patch
dpkg-source: info: applying 04_wise2-pdflatex-update.patch
dpkg-source: info: applying 05_glib2.patch
dpkg-source: info: applying 06_getline.patch
dpkg-source: info: applying 07_ld--as-needed.patch
dpkg-source: info: applying 08_mayhem.patch
dpkg-source: info: applying 09_dnal-add-return-statement.patch
dpkg-source: info: applying 10_fix_path_to_data_files.patch
dpkg-source: info: applying 11_consistent_manual_dates.patch
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying cross.patch

Check disk space
----------------

Sufficient free space for build

+------------------------------------------------------------------------------+
| Starting Timed Build Commands                                                |
+------------------------------------------------------------------------------+


ulimit -c
---------

0

I: Finished running 'ulimit -c'.

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

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
CONFIG_SITE=/etc/dpkg-cross/cross-config.amd64
DEB_BUILD_OPTIONS=nocheck
HOME=/sbuild-nonexistent
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=helmutg
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=crossqa-sid
SCHROOT_CHROOT_NAME=crossqa-sid
SCHROOT_COMMAND=env
SCHROOT_GID=1002
SCHROOT_GROUP=helmutg
SCHROOT_SESSION_ID=crossqa-sid-55208159-d16b-4353-8054-8294b5eb239f
SCHROOT_UID=1002
SCHROOT_USER=helmutg
SHELL=/bin/sh
USER=helmutg

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

Command: dpkg-buildpackage -aamd64 -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1
dpkg-buildpackage: info: source package wise
dpkg-buildpackage: info: source version 2.4.1-23
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Helmut Grohne <helmut@subdivi.de>
dpkg-architecture: warning: specified GNU system type x86_64-linux-gnu does not match CC system type aarch64-linux-gnu, try setting a correct CC environment variable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
 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 \
		\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
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>>'
dh_auto_build --sourcedirectory=src -- all
	cd src && make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=x86_64-linux-gnu-pkg-config CXX=x86_64-linux-gnu-g\+\+ CC=x86_64-linux-gnu-gcc all
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
(cd base   ; make CC="x86_64-linux-gnu-gcc" CFLAGS="-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  `x86_64-linux-gnu-pkg-config --cflags glib-2.0`" libwisebase.a )
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/base'
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include wiseconfig.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include wisestring.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include wiseerror.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include wisememman.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include wisefile.c
wisefile.dy: In function ‘Wise2_myfclose’:
wisefile.dy:72:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘FILE *’ [-Wformat=]
   72 |   fprintf(stderr,"Closing %d\n",ofp);
      |                  ^~~~~~~~~~~~~~ ~~~
      |                                 |
      |                                 FILE *
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include wiserandom.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include wisetime.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include wiseoverlay.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include wisestreaminterface.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include commandline.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include linesubs.c
ar ru libwisebase.a wiseconfig.o wisestring.o wiseerror.o wisememman.o wisefile.o wiserandom.o wisetime.o wiseoverlay.o wisestreaminterface.o commandline.o linesubs.o
ar: `u' modifier ignored since `D' is the default (see `U')
ar: creating libwisebase.a
if test -x /bin/ranlib; then /bin/ranlib libwisebase.a; else exit 0; fi
if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisebase.a; else exit 0; fi
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/base'
(cd HMMer2 ; make CC="x86_64-linux-gnu-gcc" CFLAGS="-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  `x86_64-linux-gnu-pkg-config --cflags glib-2.0`" libhmmer.a )
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/HMMer2'
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c alphabet.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c core_algorithms.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c debug.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c emit.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c emulation.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c histogram.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c hmmio.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c mathsupport.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c masks.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c misc.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c modelmakers.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c plan7.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c plan9.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c prior.c		
prior.c: In function ‘P7ReadPrior’:
prior.c:102:12: warning: implicit declaration of function ‘strcmp’ [-Wimplicit-function-declaration]
  102 |   if      (strcmp(sptr, "DIRICHLET") == 0) pri->strategy = PRI_DCHLET;
      |            ^~~~~~
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c tophits.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c trace.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c aligneval.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c alignio.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c cluster.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c dayhoff.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c file.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c getopt.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c gnuregex.c		
gnuregex.c: In function ‘re_match_2’:
gnuregex.c:3752:31: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 3752 |                           if ((int) old_regend[r] >= (int) regstart[r])
      |                               ^
gnuregex.c:3752:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 3752 |                           if ((int) old_regend[r] >= (int) regstart[r])
      |                                                      ^
gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
 2315 |   fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
      |                                          ^
gnuregex.c:2394:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
 2394 |     PUSH_FAILURE_ITEM (lowest_active_reg);    \
      |     ^~~~~~~~~~~~~~~~~
gnuregex.c:3758:19: note: in expansion of macro ‘PUSH_FAILURE_POINT’
 3758 |                   PUSH_FAILURE_POINT (p1 + mcnt, d, -2);
      |                   ^~~~~~~~~~~~~~~~~~
gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
 2315 |   fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
      |                                          ^
gnuregex.c:2397:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
 2397 |     PUSH_FAILURE_ITEM (highest_active_reg);    \
      |     ^~~~~~~~~~~~~~~~~
gnuregex.c:3758:19: note: in expansion of macro ‘PUSH_FAILURE_POINT’
 3758 |                   PUSH_FAILURE_POINT (p1 + mcnt, d, -2);
      |                   ^~~~~~~~~~~~~~~~~~
gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
 2315 |   fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
      |                                          ^
gnuregex.c:2394:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
 2394 |     PUSH_FAILURE_ITEM (lowest_active_reg);    \
      |     ^~~~~~~~~~~~~~~~~
gnuregex.c:3905:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’
 3905 |           PUSH_FAILURE_POINT (p + mcnt, NULL, -2);
      |           ^~~~~~~~~~~~~~~~~~
gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
 2315 |   fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
      |                                          ^
gnuregex.c:2397:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
 2397 |     PUSH_FAILURE_ITEM (highest_active_reg);    \
      |     ^~~~~~~~~~~~~~~~~
gnuregex.c:3905:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’
 3905 |           PUSH_FAILURE_POINT (p + mcnt, NULL, -2);
      |           ^~~~~~~~~~~~~~~~~~
gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
 2315 |   fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
      |                                          ^
gnuregex.c:2394:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
 2394 |     PUSH_FAILURE_ITEM (lowest_active_reg);    \
      |     ^~~~~~~~~~~~~~~~~
gnuregex.c:3958:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’
 3958 |           PUSH_FAILURE_POINT (p + mcnt, d, -2);
      |           ^~~~~~~~~~~~~~~~~~
gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
 2315 |   fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
      |                                          ^
gnuregex.c:2397:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
 2397 |     PUSH_FAILURE_ITEM (highest_active_reg);    \
      |     ^~~~~~~~~~~~~~~~~
gnuregex.c:3958:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’
 3958 |           PUSH_FAILURE_POINT (p + mcnt, d, -2);
      |           ^~~~~~~~~~~~~~~~~~
gnuregex.c:2482:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 2482 |   high_reg = (unsigned) POP_FAILURE_ITEM ();    \
      |              ^
gnuregex.c:4064:13: note: in expansion of macro ‘POP_FAILURE_POINT’
 4064 |             POP_FAILURE_POINT (sdummy, pdummy,
      |             ^~~~~~~~~~~~~~~~~
gnuregex.c:2485:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 2485 |   low_reg = (unsigned) POP_FAILURE_ITEM ();    \
      |             ^
gnuregex.c:4064:13: note: in expansion of macro ‘POP_FAILURE_POINT’
 4064 |             POP_FAILURE_POINT (sdummy, pdummy,
      |             ^~~~~~~~~~~~~~~~~
gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
 2315 |   fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
      |                                          ^
gnuregex.c:2394:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
 2394 |     PUSH_FAILURE_ITEM (lowest_active_reg);    \
      |     ^~~~~~~~~~~~~~~~~
gnuregex.c:4097:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’
 4097 |           PUSH_FAILURE_POINT (0, 0, -2);
      |           ^~~~~~~~~~~~~~~~~~
gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
 2315 |   fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
      |                                          ^
gnuregex.c:2397:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
 2397 |     PUSH_FAILURE_ITEM (highest_active_reg);    \
      |     ^~~~~~~~~~~~~~~~~
gnuregex.c:4097:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’
 4097 |           PUSH_FAILURE_POINT (0, 0, -2);
      |           ^~~~~~~~~~~~~~~~~~
gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
 2315 |   fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
      |                                          ^
gnuregex.c:2394:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
 2394 |     PUSH_FAILURE_ITEM (lowest_active_reg);    \
      |     ^~~~~~~~~~~~~~~~~
gnuregex.c:4110:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’
 4110 |           PUSH_FAILURE_POINT (0, 0, -2);
      |           ^~~~~~~~~~~~~~~~~~
gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
 2315 |   fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
      |                                          ^
gnuregex.c:2397:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
 2397 |     PUSH_FAILURE_ITEM (highest_active_reg);    \
      |     ^~~~~~~~~~~~~~~~~
gnuregex.c:4110:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’
 4110 |           PUSH_FAILURE_POINT (0, 0, -2);
      |           ^~~~~~~~~~~~~~~~~~
gnuregex.c:2482:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 2482 |   high_reg = (unsigned) POP_FAILURE_ITEM ();    \
      |              ^
gnuregex.c:4278:11: note: in expansion of macro ‘POP_FAILURE_POINT’
 4278 |           POP_FAILURE_POINT (d, p,
      |           ^~~~~~~~~~~~~~~~~
gnuregex.c:2485:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 2485 |   low_reg = (unsigned) POP_FAILURE_ITEM ();    \
      |             ^
gnuregex.c:4278:11: note: in expansion of macro ‘POP_FAILURE_POINT’
 4278 |           POP_FAILURE_POINT (d, p,
      |           ^~~~~~~~~~~~~~~~~
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c interleaved.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c iupac.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c msf.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c revcomp.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c selex.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c sqerror.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c sqio.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c sre_ctype.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c sre_math.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c sre_string.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c stack.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c translate.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c types.c		
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include  -c weight.c		
ar rcv  libhmmer.a alphabet.o    core_algorithms.o debug.o	          emit.o emulation.o   histogram.o       hmmio.o           mathsupport.o masks.o       misc.o            modelmakers.o     plan7.o plan9.o       prior.o           tophits.o         trace.o aligneval.o   alignio.o         cluster.o         dayhoff.o file.o        getopt.o          gnuregex.o        interleaved.o iupac.o       msf.o             revcomp.o         selex.o sqerror.o     sqio.o            sre_ctype.o       sre_math.o sre_string.o  stack.o           translate.o       types.o weight.o
a - alphabet.o
a - core_algorithms.o
a - debug.o
a - emit.o
a - emulation.o
a - histogram.o
a - hmmio.o
a - mathsupport.o
a - masks.o
a - misc.o
a - modelmakers.o
a - plan7.o
a - plan9.o
a - prior.o
a - tophits.o
a - trace.o
a - aligneval.o
a - alignio.o
a - cluster.o
a - dayhoff.o
a - file.o
a - getopt.o
a - gnuregex.o
a - interleaved.o
a - iupac.o
a - msf.o
a - revcomp.o
a - selex.o
a - sqerror.o
a - sqio.o
a - sre_ctype.o
a - sre_math.o
a - sre_string.o
a - stack.o
a - translate.o
a - types.o
a - weight.o
if test -x /bin/ranlib; then /bin/ranlib libhmmer.a; else exit 0; fi
if test -x /usr/bin/ranlib; then /usr/bin/ranlib libhmmer.a; else exit 0; fi
if test -x ranlib; then ranlib libhmmer.a; else exit 0; fi
chmod 644 libhmmer.a
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/HMMer2'
(cd dynlibsrc ; make CC="x86_64-linux-gnu-gcc" CFLAGS="-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  `x86_64-linux-gnu-pkg-config --cflags glib-2.0`" libdyna.a )
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/dynlibsrc'
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ packaln.c
packaln.dy: In function ‘Wise2_read_simple_PackAln’:
packaln.dy:88:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   88 |   fgets(buffer,MAXLINE,ifp);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ aln.c
aln.dy: In function ‘Wise2_mapped_ascii_AlnBlock’:
aln.dy:867:19: warning: too many arguments for format [-Wformat-extra-args]
  867 |       fprintf(ofp," {%3.2f}  ",(double)(*score_to_double)(cuml),cuml);
      |                   ^~~~~~~~~~~~
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ dnamatrix.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ probability.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ alnrange.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ alnconvert.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ basematrix.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ shattermatrix.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ matrixdebug.c
matrixdebug.dy: In function ‘Wise2_user_DebugMatrix’:
matrixdebug.dy:208:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  208 |     fgets(buffer,MAXLINE,in);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ dpenvelope.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ dbsearchimpl.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ dprunimpl.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ complexsequence.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ complexevalset.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ complexconsensi.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ sequence.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ sequencestream.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ seqalign.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ hitlist.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ hsp.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ hspstream.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ codon.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ compmat.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ codonmatrix.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ codonmapper.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ sequencedb.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ hscore.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ seqlookup.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ arrayseqlookup.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ genericindexresult.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ linkedlist_lookpos.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ singlenumberspace.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ histogram.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ searchstatinterface.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ searchstatlookup.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ proteindb.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ protein.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ pairbase.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ pairbaseseq.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ genomicdb.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ randommodel.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ randomdb.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ genomic.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ cdna.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ cdnadb.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ dna.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ embl.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ genomicregion.c
genomicregion.dy: In function ‘Wise2_read_EMBL_FT_into_GenomicRegion’:
genomicregion.dy:756:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  756 |   fgets(buffer,maxlen,ifp);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ gene.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ transcript.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ translation.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ btcanvas.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ asciibtcanvas.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ dynlibcross.c
ar ru libdyna.a packaln.o aln.o dnamatrix.o probability.o alnrange.o alnconvert.o basematrix.o shattermatrix.o matrixdebug.o dpenvelope.o dbsearchimpl.o dprunimpl.o complexsequence.o complexevalset.o complexconsensi.o sequence.o sequencestream.o seqalign.o hitlist.o hsp.o hspstream.o codon.o compmat.o codonmatrix.o codonmapper.o sequencedb.o hscore.o seqlookup.o arrayseqlookup.o genericindexresult.o linkedlist_lookpos.o singlenumberspace.o histogram.o searchstatinterface.o searchstatlookup.o proteindb.o protein.o pairbase.o pairbaseseq.o genomicdb.o randommodel.o randomdb.o genomic.o cdna.o cdnadb.o dna.o embl.o genomicregion.o gene.o transcript.o translation.o btcanvas.o asciibtcanvas.o dynlibcross.o
ar: `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="x86_64-linux-gnu-gcc" CFLAGS="-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  `x86_64-linux-gnu-pkg-config --cflags glib-2.0`" libdyna_glib.a )
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/dynlibsrc'
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ subseqhash.c
subseqhash.dy: In function ‘Wise2_is_populated_subseqhash_ghash’:
subseqhash.dy:111:29: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  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);
      |                           ^
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ intallocator.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ proteinstreamedindex.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ shadowseq.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ shadowseqindex.c
shadowseqindex.dy: In function ‘Wise2_dump_stats_ShadowSequenceIndex’:
shadowseqindex.dy:285:15: 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
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ hsphandler.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ hspscaninterface.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ hsp2hitscan.c
hsp2hitscan.dy: In function ‘Wise2_one_off_two_hit_HSPscan_query_direct’:
hsp2hitscan.dy: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=]
hsp2hitscan.dy:209:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘__time_t’ {aka ‘long int’} [-Wformat=]
hsp2hitscan.dy:209:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘__time_t’ {aka ‘long int’} [-Wformat=]
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=]
hsp2hitscan.dy:273:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘__time_t’ {aka ‘long int’} [-Wformat=]
hsp2hitscan.dy:273:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘__time_t’ {aka ‘long int’} [-Wformat=]
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=]
hsp2hitscan.dy:286:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘__time_t’ {aka ‘long int’} [-Wformat=]
hsp2hitscan.dy:286:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘__time_t’ {aka ‘long int’} [-Wformat=]
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=]
hsp2hitscan.dy:302:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘__time_t’ {aka ‘long int’} [-Wformat=]
hsp2hitscan.dy:302:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘__time_t’ {aka ‘long int’} [-Wformat=]
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ hsplookupscan.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ hsplookupthreaded.c
hsplookupthreaded.dy: In function ‘Wise2_one_off_ordered_HSPscan_scan_query_direct’:
hsplookupthreaded.dy:263:18: 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
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ hspthreadeddb.c
hspthreadeddb.dy: In function ‘Wise2_threadeddb_scan_worker’:
hspthreadeddb.dy:154:77: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  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 *
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ hspscanruntime.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ hsptwohitscan.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ proteinindexcons.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ dnaindexcons.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ staticseq.c
ar ru libdyna_glib.a subseqhash.o intallocator.o proteinstreamedindex.o shadowseq.o shadowseqindex.o hsphandler.o hspscaninterface.o hsp2hitscan.o hsplookupscan.o hsplookupthreaded.o hspthreadeddb.o hspscanruntime.o hsptwohitscan.o proteinindexcons.o dnaindexcons.o staticseq.o
ar: `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="x86_64-linux-gnu-gcc" CFLAGS="-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  `x86_64-linux-gnu-pkg-config --cflags glib-2.0`" all )
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/external'
(cd mott; make CC="x86_64-linux-gnu-gcc" CFLAGS="-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include" all)
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/external/mott'
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -Wdate-time -D_FORTIFY_SOURCE=2  -c -o mott_api.o mott_api.c
mott_api.c: In function ‘InitPvaluesMott’:
mott_api.c:64:3: warning: implicit declaration of function ‘free’ [-Wimplicit-function-declaration]
   64 |   free(freq0);
      |   ^~~~
mott_api.c:64:3: warning: incompatible implicit declaration of built-in function ‘free’
mott_api.c:5:1: note: include ‘<stdlib.h>’ or provide a declaration of ‘free’
    4 | #include"gapstat.h"
  +++ |+#include <stdlib.h>
    5 | 
mott_api.c: In function ‘SW_PValueMott’:
mott_api.c:104:7: warning: incompatible implicit declaration of built-in function ‘free’
  104 |       free(freqA);
      |       ^~~~
mott_api.c:104:7: note: include ‘<stdlib.h>’ or provide a declaration of ‘free’
mott_api.c: In function ‘KarlinAltschulStatistics2’:
mott_api.c:144:5: warning: incompatible implicit declaration of built-in function ‘free’
  144 |     free(h+hmin);
      |     ^~~~
mott_api.c:144:5: note: include ‘<stdlib.h>’ or provide a declaration of ‘free’
mott_api.c:155:5: warning: incompatible implicit declaration of built-in function ‘free’
  155 |     free(h+hmin);
      |     ^~~~
mott_api.c:155:5: note: include ‘<stdlib.h>’ or provide a declaration of ‘free’
mott_api.c: In function ‘GetHistogram’:
mott_api.c:179:16: warning: implicit declaration of function ‘calloc’ [-Wimplicit-function-declaration]
  179 |   h = (double*)calloc(*hmax-*hmin+1,sizeof(double))-*hmin;
      |                ^~~~~~
mott_api.c:179:16: warning: incompatible implicit declaration of built-in function ‘calloc’
mott_api.c:179:16: note: include ‘<stdlib.h>’ or provide a declaration of ‘calloc’
mott_api.c: In function ‘PseudoResidueFrequencies2’:
mott_api.c:207:12: warning: implicit declaration of function ‘toupper’ [-Wimplicit-function-declaration]
  207 |       freq[toupper(seq[n])]++;
      |            ^~~~~~~
mott_api.c: In function ‘RobinsonResidueFrequencies2’:
mott_api.c:230:27: warning: incompatible implicit declaration of built-in function ‘calloc’
  230 |   double *freq = (double*)calloc(256, sizeof(double));
      |                           ^~~~~~
mott_api.c:230:27: note: include ‘<stdlib.h>’ or provide a declaration of ‘calloc’
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -Wdate-time -D_FORTIFY_SOURCE=2  -c -o gaplib.o gaplib.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../../dynlibsrc -I../../base wise2_mott_bridge.c
ar ru libmott.a mott_api.o gaplib.o wise2_mott_bridge.o
ar: `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="x86_64-linux-gnu-gcc" CFLAGS="-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  `x86_64-linux-gnu-pkg-config --cflags glib-2.0`" libwisesocket.a )
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/socket'
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ functionserver.c
functionserver.dy: In function ‘Wise2_main_loop_forking_FunctionServer’:
functionserver.dy:129:4: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  129 |    write(new_socket,buf,9);
      |    ^~~~~~~~~~~~~~~~~~~~~~~
functionserver.dy:141:2: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  141 |  write(new_socket,buf,6);
      |  ^~~~~~~~~~~~~~~~~~~~~~~
functionserver.dy:183:2: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  183 |  write(new_socket,buf,5);
      |  ^~~~~~~~~~~~~~~~~~~~~~~
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ functionclient.c
functionclient.dy: In function ‘Wise2_new_FunctionProxyCoordinator’:
functionclient.dy:193:24: warning: passing argument 2 of ‘connect’ from incompatible pointer type [-Wincompatible-pointer-types]
  193 |   connect(out->socket, &server, sizeof(server));
      |                        ^~~~~~~
      |                        |
      |                        struct sockaddr_in *
In file included from functionclient.c:7:
/usr/x86_64-linux-gnu/include/sys/socket.h:126:52: note: expected ‘const struct sockaddr *’ but argument is of type ‘struct sockaddr_in *’
  126 | extern int connect (int __fd, __CONST_SOCKADDR_ARG __addr, socklen_t __len);
      |                                                    ^
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ anonobj.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ transferinterface.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ directsocketwrite.c
ar ru libwisesocket.a functionserver.o functionclient.o anonobj.o transferinterface.o directsocketwrite.o
ar: `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="x86_64-linux-gnu-gcc" CFLAGS="-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  `x86_64-linux-gnu-pkg-config --cflags glib-2.0`" all )
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/dnaindex'
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly.c
kmer_assembly.dy: In function ‘Wise2_show_KmerAssemblyNode’:
kmer_assembly.dy:296:15: 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]);
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_index_interface.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_direct.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_hash.c
kmer_hash.dy: In function ‘Wise2_free_KmerHashIndex’:
kmer_hash.dy:318:19: 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}
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_count.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_glib_index.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models singleseqspace.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models dnamapping.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models largeseqreader.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_untangler.c
kmer_assembly_untangler.dy: In function ‘Wise2_show_KmerAssemblyPath’:
kmer_assembly_untangler.dy:52:65: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
   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=]
kmer_assembly_untangler.dy:157:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=]
  157 |       fprintf(stderr,"RESOLVED: Node %ld [%s] Fully untangled now...\n",node->number,buffer);
      |                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~
      |                                                                             |
      |                                                                             kmer_t {aka long long int}
kmer_assembly_untangler.dy:159:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=]
  159 |       fprintf(stderr,"UNRESOLVED: Node %ld [%s] still tangled...\n",node->number,buffer);
      |                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~
      |                                                                         |
      |                                                                         kmer_t {aka long long int}
kmer_assembly_untangler.dy: In function ‘Wise2_old_attempt_forward_untangle_KmerAssembly’:
kmer_assembly_untangler.dy:444:20: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=]
  444 |     fprintf(stderr,"looking at node %ld with path length %d, next length %d depth %d\n",current->next->number,pathlen,current->next->next_len,current->sequence_label_len);
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~
      |                                                                                                      |
      |                                                                                                      kmer_t {aka long long int}
kmer_assembly_untangler.dy:568:75: warning: passing argument 4 of ‘Wise2_lift_backward_tangled_tail’ from incompatible pointer type [-Wincompatible-pointer-types]
  568 |  lift_backward_tangled_tail(kai,newpath->stack[newpath->stack_len-1],path,transferred_label,transferred_pos,transferred_len);
      |                                                                           ^~~~~~~~~~~~~~~~~
      |                                                                           |
      |                                                                           long int *
In file included from kmer_assembly_untangler.c:4:
kmer_assembly_untangler.h:174:116: note: expected ‘int *’ but argument is of type ‘long int *’
  174 | void Wise2_lift_backward_tangled_tail(KmerAssemblyIndex * kai,KmerAssemblyLink * new,KmerAssemblyPath * tail,int * start_label,SinglePosSequence ** positions,int label_len);
      |                                                                                                              ~~~~~~^~~~~~~~~~~
kmer_assembly_untangler.dy: In function ‘Wise2_lift_forward_tangled_KmerAssemblyPath’:
kmer_assembly_untangler.dy:746:20: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 6 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=]
  746 |     fprintf(stderr,"Moving stack position %d, depth %d, transfer %d, between %ld [%s] and %ld [%s]\n",i,kap->stack[i]->sequence_label_len,label_len,kap->stack[i]->prev->number,back,kap->stack[i]->next->number,forw);
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                                               ~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                                                                                                                        |
      |                                                                                                                                                                        kmer_t {aka long long int}
kmer_assembly_untangler.dy:746:20: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 8 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=]
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_contig.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_error.c
kmer_assembly_error.dy: In function ‘Wise2_mark_tangles_KmerAssembly’:
kmer_assembly_error.dy:93:22: 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:351:17: 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 *
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models compressed_protein_index.c
compressed_protein_index.dy: In function ‘Wise2_add_direct_number_CompressedProteinIndex’:
compressed_protein_index.dy:223:10: warning: returning ‘void *’ from a function with return type ‘boolean’ {aka ‘int’} makes integer from pointer without a cast [-Wint-conversion]
  223 |   return NULL;
      |          ^~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/dnaindex'
(cd network ; make  CC="x86_64-linux-gnu-gcc" CFLAGS="-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  `x86_64-linux-gnu-pkg-config --cflags glib-2.0`" all )
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/network'
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/  -I../socket -I../dynlibsrc -I../dnaindex wise_proteinindex_server.c
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);
      |                                                                                                       ^~~~~~~~~~~~
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/  -I../socket -I../dynlibsrc -I../dnaindex net_hspscan.c
x86_64-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 `x86_64-linux-gnu-pkg-config --libs glib-2.0` -lpthread 
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/  -I../socket -I../dynlibsrc -I../dnaindex client_multihspscan.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/network'
(cd models  ; make CC="x86_64-linux-gnu-gcc" CFLAGS="-g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  `x86_64-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'
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dnal.c
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);
      |                                                                                                       ^~~~~~~~~~~~
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dnaalign.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ seqaligndisplay.c
x86_64-linux-gnu-gcc -o dnal dnal.o dnaalign.o seqaligndisplay.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `x86_64-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ psw.c
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);
      |                                                                                                       ^~~~~~~~~~~~
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ proteinsw.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ sw_wrap.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ abc.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pba.c
x86_64-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 `x86_64-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pswdb.c
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);
      |                                                                                                          ^~~~~~~~~~~~
x86_64-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 `x86_64-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dbac.c
dbac.c: In function ‘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
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dba.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ slimdba.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ bigdba.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dbadisplay.c
x86_64-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 `x86_64-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include estwise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I.
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);
      |                                                                                                       ^~~~~~~~~~~~
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparser21.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparameter.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genestats.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisehsp.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneutil.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneoutput.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ threestatemodel.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genefrequency.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ splicesitemodeler.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise4.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise6.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genestretch6.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise21.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneloop21.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneloop6.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genephase6.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ gwlite.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ gwlitemodel.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ gwrap.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ matchsum.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estwrap.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisemodel.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ phasemodel.c
phasemodel.dy: In function ‘Wise2_read_fasta_PhasedProtein’:
phasemodel.dy:241:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  241 |   fgets(name,10000,ifp);
      |   ^~~~~~~~~~~~~~~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/stdio.h:867,
                 from ../base/wisebase.h:6,
                 from ../dynlibsrc/probability.h:7,
                 from geneparser21.h:6,
                 from genewisemodel.h:6,
                 from phasemodel.h:6,
                 from phasemodel.c:4:
In function ‘fgets’,
    inlined from ‘Wise2_read_fasta_PhasedProtein’ at phasemodel.dy:241:3:
/usr/x86_64-linux-gnu/include/bits/stdio2.h:263:9: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning]
  263 |  return __fgets_chk_warn (__s, __bos (__s), __n, __stream);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ cdparser.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genedisplay.c
genedisplay.dy: In function ‘Wise2_write_intron_desc’:
genedisplay.dy:493:20: warning: too many arguments for format [-Wformat-extra-args]
  493 |     sprintf(buffer,"  Intron ???  ",in_number);
      |                    ^~~~~~~~~~~~~~~~
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estwise3.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estslim3.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estloop3.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estfrag3.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estslimloop.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ gwquickdb.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ threestatedb.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pfamhmmer1db.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pwmdna.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../HMMer2/ -DHMMER_INTERNAL -I../base/ -I../dynlibsrc/ wise2xhmmer2.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisemodeldb.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ seqhit.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ standardout.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparser4.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estquick3.c
x86_64-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 `x86_64-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 `x86_64-linux-gnu-pkg-config --libs glib-2.0`
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include genewise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I.
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);
      |                                                                                                       ^~~~~~~~~~~~
x86_64-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 `x86_64-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 `x86_64-linux-gnu-pkg-config --libs glib-2.0`
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include genewisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ 
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);
      |                                                                                                       ^~~~~~~~~~~~
x86_64-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 `x86_64-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 `x86_64-linux-gnu-pkg-config --libs glib-2.0`
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include estwisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/
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);
      |                                                                                                       ^~~~~~~~~~~~
x86_64-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 `x86_64-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 `x86_64-linux-gnu-pkg-config --libs glib-2.0`
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genomewise.c
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);
      |                                                                                                       ^~~~~~~~~~~~
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genomewise9.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genome_evidence.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ est_evidence.c
est_evidence.dy: In function ‘Wise2_new_est_GenomeEvidenceUnit’:
est_evidence.dy:142:16: warning: assignment to ‘int (*)(void *)’ from incompatible pointer type ‘Wise2_EstEvidence * (*)(Wise2_EstEvidence *)’ [-Wincompatible-pointer-types]
  142 |   in->geu_free = free_EstEvidence;
      |                ^
x86_64-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 `x86_64-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ sywise.c
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);
      |                                                                                                       ^~~~~~~~~~~~
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ sywise20.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ syexonmodel.c
x86_64-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 `x86_64-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pseudowise.c
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);
      |                                                                                                       ^~~~~~~~~~~~
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pseudowise7.c
x86_64-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 `x86_64-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 `x86_64-linux-gnu-pkg-config --libs glib-2.0`
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ `x86_64-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);
      |                                                                                                       ^~~~~~~~~~~~
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ localdba.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ `x86_64-linux-gnu-pkg-config --cflags glib-2.0` localcishit.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ localcispara.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ motifmatrix.c
motifmatrix.c: In function ‘Wise2_MotifConsMatrix_alloc_matrix’:
motifmatrix.c:408:24: warning: assignment to ‘char’ from ‘void *’ makes integer from pointer without a cast [-Wint-conversion]
  408 |     for(i=0;i<leni;i++)  {
      |                        ^
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ motifmatrixdp.c
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ 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/x86_64-linux-gnu/include/stdio.h:867,
                 from ../base/wisebase.h:6,
                 from pwmdna.h:6,
                 from transfactor.h:6,
                 from transfactor.c:4:
/usr/x86_64-linux-gnu/include/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 9 and 529 bytes into a destination of size 512
   36 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   37 |       __bos (__s), __fmt, __va_arg_pack ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pairwiseshortdna.c
x86_64-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 `x86_64-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm `x86_64-linux-gnu-pkg-config --libs glib-2.0` -lpthread
x86_64-linux-gnu-gcc  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/  -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);
      |                                                                                                       ^~~~~~~~~~~~
x86_64-linux-gnu-gcc -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ `x86_64-linux-gnu-pkg-config --cflags glib-2.0` hsp2aln_sw.c
x86_64-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 `x86_64-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 `x86_64-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 3.14159265-2.6-1.40.21 (TeX Live 2020/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./api.tex
LaTeX2e <2020-10-01> patch level 4
L3 programming layer <2021-01-09> xparse <2020-03-03>
(/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 2020/04/10 v1.4m 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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[6]

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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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[10]

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[11]

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\OT1/cmr/m/n/10 AlnBlock is the main rep-re-sen-ta-tion of align-ments from Dy-
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[20]

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[21] [22] [23] [24]

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e 1363.


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[28]
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LaTeX Warning: Reference `object_ComplexSequence' on page 29 undefined on input
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[29]

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ne 1624.

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LaTeX Warning: Reference `object_DnaProbMatrix' on page 34 undefined on input l
ine 1738.

[34]

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LaTeX Warning: Reference `object_GenomicRepeat' on page 38 undefined on input l
ine 1950.

[38]
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[]\OT1/cmtt/m/n/10 Wise2[]Genomic[]from[]Sequence[]Nheuristic (seq,length[]of[]
N) 

LaTeX Warning: Reference `accessing_fields' on page 39 undefined on input line 
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[41]

LaTeX Warning: Reference `object_GenomicDB' on page 42 undefined on input line 
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[]\OT1/cmtt/m/n/10 Wise2[]new[]GenomicDB[]from[]single[]seq (gen,cses,score[]in
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[]\OT1/cmtt/m/n/10 &Wise2::new[]GenomicDB[]from[]single[]seq (gen,cses,score[]i
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[]\OT1/cmtt/m/n/10 Wise2[]new[]GenomicDB (seqdb,cses,length[]of[]N,repeat[]in[]
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[]\OT1/cmtt/m/n/10 &Wise2::new[]GenomicDB (seqdb,cses,length[]of[]N,repeat[]in[
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[42]

LaTeX Warning: Reference `accessing_fields' on page 43 undefined on input line 
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[43]

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[44]
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[]\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::read[]EMBL[]GenomicRegion[]file (file
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[45]
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[]\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::show[]ace[]GenomicRegion (gr,seq[]nam
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[]\OT1/cmtt/m/n/10 Wise2[]show[]pretty[]GenomicRegion (gr,show[]supporting,ofp)
 

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[46] [47]

LaTeX Warning: Reference `object_Histogram' on page 48 undefined on input line 
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[48]

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[]   \OT1/cmtt/m/n/10 b) cooperation with future versions of histogram.c would 
be possible.[] 
[49] [50] [51]
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[]\OT1/cmtt/m/n/10 Wise2[]ExtremeValueSetHistogram (h,mu,lambda,lowbound,highbo
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[]\OT1/cmtt/m/n/10 &Wise2::Histogram::set[]EVD (h,mu,lambda,lowbound,highbound,
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[]\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->set[]EVD(mu,lambda,lowbound,highbound
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[52] [53] [54]

LaTeX Warning: Reference `object_Hscore' on page 55 undefined on input line 293
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e 3231.


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LaTeX Warning: Reference `object_Protein' on page 63 undefined on input line 34
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[65]

LaTeX Warning: Reference `object_RandomModelDNA' on page 66 undefined on input 
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[66]

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LaTeX Warning: Reference `object_Sequence' on page 67 undefined on input line 3
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[67]

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[68]
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[]\OT1/cmtt/m/n/10 Wise2[]force[]to[]dna[]Sequence (seq,fraction,number[]of[]co
nver) 
[69] [70] [71] [72] [73] [74]

LaTeX Warning: Reference `accessing_fields' on page 75 undefined on input line 
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LaTeX Warning: Reference `object_Exon' on page 78 undefined on input line 4381.



LaTeX Warning: Reference `object_Transcript' on page 78 undefined on input line
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[78]

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LaTeX Warning: Reference `object_Translation' on page 80 undefined on input lin
e 4482.


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\OT1/cmr/m/n/10 have any se-quence in it. When se-quence is asked for by get[]P
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[80]

LaTeX Warning: Reference `object_cDNAParser' on page 81 undefined on input line
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[81]

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e 4602.


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[]\OT1/cmtt/m/n/10 Wise2[]make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap,
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[]\OT1/cmtt/m/n/10 &Wise2::make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap
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[82]

LaTeX Warning: Reference `accessing_fields' on page 83 undefined on input line 
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[]\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]TSM[]estwise (tdb,cdb,cp,cm,rmd,use[]sy
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[]\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]TSM[]estwise (tdb,cdb,cp,cm,rmd,use[]s
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[83]
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[]\OT1/cmtt/m/n/10 Wise2[]AlnBlock[]from[]Protein[]estwise[]wrap (pro,cdna,cp,c
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[]\OT1/cmtt/m/n/10 &Wise2::AlnBlock[]from[]Protein[]estwise[]wrap (pro,cdna,cp,
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[84]
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[]\OT1/cmtt/m/n/10 &Wise2::AlnBlock[]from[]TSM[]estwise[]wrap (tsm,cdna,cp,cm,c
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[85]
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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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[86]
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[]\OT1/cmtt/m/n/10 Wise2[]protcdna[]ascii[]display (alb,protsequence,protname,p
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[]\OT1/cmtt/m/n/10 &Wise2::protcdna[]ascii[]display (alb,protsequence,protname,
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LaTeX Warning: Reference `object_GeneFrequency21' on page 87 undefined on input
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LaTeX Warning: Reference `object_GeneConsensus' on page 87 undefined on input l
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LaTeX Warning: Reference `object_GeneSingleCons' on page 87 undefined on input 
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[87]

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[]\OT1/cmr/m/n/10 transition[GENEFREQUENCY21[]TRANSITION[]LEN] Type [dou-ble : 
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LaTeX Warning: Reference `accessing_fields' on page 88 undefined on input line 
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[89]

LaTeX Warning: Reference `object_MatchSummarySet' on page 90 undefined on input
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[]\OT1/cmtt/m/n/10 &Wise2::MatchSummarySet::MatchSummarySet[]from[]AlnBlock[]es
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[]\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->MatchSummarySet[]from[]AlnBlock[]gene
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LaTeX Warning: Reference `accessing_fields' on page 91 undefined on input line 
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[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
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[92]
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[]\OT1/cmtt/m/n/10 Wise2[]write[]pretty[]str[]align (alb,qname,query,tname,targ
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[]\OT1/cmtt/m/n/10 &Wise2::write[]pretty[]str[]align (alb,qname,query,tname,tar
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[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
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LaTeX Warning: Reference `object_SegmentHitList' on page 94 undefined on input 
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LaTeX Warning: Reference `object_SegmentHit' on page 94 undefined on input line
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[94]

LaTeX Warning: Reference `accessing_fields' on page 95 undefined on input line 
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[]\OT1/cmtt/m/n/10 &Wise2::DnaSequenceHitList::read[]MSPcrunch[]DnaSequenceHitL
ist (ifp) 
[95]

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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
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[96]
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[]\OT1/cmtt/m/n/10 Wise2[]Align[]Sequences[]ProteinSmithWaterman (one,two,comp,
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[]\OT1/cmtt/m/n/10 &Wise2::Align[]Sequences[]ProteinSmithWaterman (one,two,comp
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[]\OT1/cmr/m/n/10 [OWNER] new AlnBlock struc-ture rep-re-sent-ing the align-men
t [AlnBlock
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[]\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]SmithWaterman (one,two,comp,gap,ext,
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[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
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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
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[99]
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[100]
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[]\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinBA (querydb,targetdb,comp,bentry
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[]\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinBA (querydb,targetdb,comp,bentr
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LaTeX Warning: Reference `object_ThreeStateDB' on page 101 undefined on input l
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LaTeX Warning: Reference `accessing_fields' on page 101 undefined on input line
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[101]
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[]\OT1/cmr/m/n/10 reload[]generic Type [Three-State-Model * (*reload[]generic)(
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[]\OT1/cmr/m/n/10 dataentry[]add Type [boolean (*dataen-try[]add)(ThreeStateDB 
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[]\OT1/cmr/m/n/10 index[]generic Type [Three-State-Model * (*in-dex[]generic)(T
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[]\OT1/cmtt/m/n/10 &Wise2::ThreeStateDB::new[]proteindb[]ThreeStateDB (sdb,comp
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[103] [104]

LaTeX Warning: Reference `object_ThreeStateModel' on page 105 undefined on inpu
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LaTeX Warning: Reference `object_ThreeStateUnit' on page 105 undefined on input
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LaTeX Warning: Reference `accessing_fields' on page 105 undefined on input line
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[105]
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[]\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::force[]global[]model (tsm,prob[]int
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[]\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->force[]weighted[]local[]model(prob[]i
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[106]
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[]\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::write[]HMMer[]1[]7[]ascii[]ThreeSta
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[107] [108] (./api.aux)
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cd docs && pdflatex api.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.21 (TeX Live 2020/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./api.tex
LaTeX2e <2020-10-01> patch level 4
L3 programming layer <2021-01-09> xparse <2020-03-03>
(/usr/share/texlive/texmf-dist/tex/latex/base/latex209.def

          Entering LaTeX 2.09 COMPATIBILITY MODE
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    !!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)
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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]

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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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\OT1/cmr/m/n/10 AlnBlock is the main rep-re-sen-ta-tion of align-ments from Dy-
na-mite. Each AlnBlock
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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
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[53]
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e,ofp) 

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[54] [55] [56]
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[]   \OT1/cmtt/m/n/10 b) cooperation with future versions of histogram.c would 
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[]\OT1/cmtt/m/n/10 Wise2[]ExtremeValueSetHistogram (h,mu,lambda,lowbound,highbo
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[]\OT1/cmtt/m/n/10 &Wise2::Histogram::set[]EVD (h,mu,lambda,lowbound,highbound,
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[]\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->set[]EVD(mu,lambda,lowbound,highbound
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[]\OT1/cmr/m/n/10 should[]store Type [boolean (*should[]store)(int given[]score
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[]\OT1/cmtt/m/n/10 Wise2[]force[]to[]dna[]Sequence (seq,fraction,number[]of[]co
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\OT1/cmr/m/n/10 have any se-quence in it. When se-quence is asked for by get[]P
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text,dpri) 

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[90]
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[]\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]TSM[]estwise (tdb,cdb,cp,cm,rmd,use[]sy
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[]\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]TSM[]estwise (tdb,cdb,cp,cm,rmd,use[]s
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[91]
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[]\OT1/cmtt/m/n/10 Wise2[]AlnBlock[]from[]Protein[]estwise[]wrap (pro,cdna,cp,c
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[]\OT1/cmtt/m/n/10 &Wise2::AlnBlock[]from[]Protein[]estwise[]wrap (pro,cdna,cp,
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[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
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[]\OT1/cmtt/m/n/10 &Wise2::protcdna[]ascii[]display (alb,protsequence,protname,
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[95]
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[]\OT1/cmr/m/n/10 transition[GENEFREQUENCY21[]TRANSITION[]LEN] Type [dou-ble : 
Scalar]
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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
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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,
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[]\OT1/cmtt/m/n/10 &Wise2::MatchSummarySet::MatchSummarySet[]from[]AlnBlock[]ge
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[]\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->MatchSummarySet[]from[]AlnBlock[]gene
wise(qname,protoff,target) 
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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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[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
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[]\OT1/cmr/m/n/10 [OWNER] new AlnBlock struc-ture rep-re-sent-ing the align-men
t [AlnBlock
[105]
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[]\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]SmithWaterman (one,two,comp,gap,ext,
dpenv,dpri) 

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[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
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[]\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b,
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[108]
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[]\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinBA (querydb,targetdb,comp,bentry
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[]\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinBA (querydb,targetdb,comp,bentr
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[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
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[110]
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[]\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) 

Overfull \hbox (49.31339pt too wide) in paragraph at lines 5845--5846
[]\OT1/cmtt/m/n/10 Wise2[]ThreeStateModel[]from[]half[]bit[]Sequence (pro,mat,r
m,gap,ext) 
[114]
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[]\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::ThreeStateModel[]from[]half[]bit[]S
equence

Overfull \hbox (39.75452pt too wide) in paragraph at lines 5848--5849
[]\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->ThreeStateModel[]from[]half[]bit[]Seq
uence(mat,rm,gap,ext) 

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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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Output written on api.pdf (116 pages, 313009 bytes).
Transcript written on api.log.
cd docs && pdflatex dynamite.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.21 (TeX Live 2020/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./dynamite.tex
LaTeX2e <2020-10-01> patch level 4
L3 programming layer <2021-01-09> xparse <2020-03-03>
(/usr/share/texlive/texmf-dist/tex/latex/base/latex209.def

          Entering LaTeX 2.09 COMPATIBILITY MODE
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    !!WARNING!!    !!WARNING!!    !!WARNING!!    !!WARNING!!   
 
 This mode attempts to provide an emulation of the LaTeX 2.09
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 Therefore such style files MUST BE UPDATED to use
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 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.
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(/usr/share/texlive/texmf-dist/tex/latex/base/tracefnt.sty)
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[2] [3]

LaTeX Warning: Reference `own_objects' on page 4 undefined on input line 77.

[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]
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[] 

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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]
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.[] 

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[]    \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);[] 

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[]   \OT1/cmtt/m/n/10 * If the sequences are small enough then it should use ex
plicit memory.[] 
[13]
Overfull \hbox (59.24648pt too wide) in paragraph at lines 588--588
[]  \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp
,-gap,-ext,NULL);[] 

Overfull \hbox (80.24629pt too wide) in paragraph at lines 588--588
[]    \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query
->name,target->name);[] 
[14]
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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]
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);[] 

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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]
Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738
[]\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[] 

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[] 

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[]                     \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[] 

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[]\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))"[] 

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[]          \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);[] 

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[]   \OT1/cmtt/m/n/10 * To do this we need a cdna ComplexSequenceEvalSet and a 
genomic one[] 

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[]   \OT1/cmtt/m/n/10 * Really our genomic model should be alot more complex. T
he 'default' one[] 

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[]   \OT1/cmtt/m/n/10 * has 0 at GT----AG for 5' and 3' splice sites, and NEGI 
(= -infinity)[] 

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[]   \OT1/cmtt/m/n/10 * We could build up something much better, using complexc
onsensi and[] 

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[]   \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[] 

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[]   \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[] 

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[]   \OT1/cmtt/m/n/10 * of what is thought to be sequencing error and the intro
ns. Here we have[] 

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[]   \OT1/cmtt/m/n/10 * one more parameter, and intron open penalty, which can 
be set, to prevent[] 

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[]   \OT1/cmtt/m/n/10 * One good way to parameterise all this would be to have 
a probabilistic[] 

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[]   \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[] 

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[]   \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[] 

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[]    \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[] 

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[]                     \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[] 

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[]                     \OT1/cmtt/m/n/10 CTCCGTGGATAAGATTGTCA             TTCAGA
AATACCATAC[] 

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[]\OT1/cmtt/m/n/10 HSHNRNPA        2275 CTCCGTGGATAAGATTGTCA<-2295:2387->TTCAGA
AATACCATAC[] 

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[]\OT1/cmtt/m/n/10 HSHNCPA1        182  TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC
AAAGCAAGAG[] 

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[]                     \OT1/cmtt/m/n/10 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC
AAAGCAAGAG[] 

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[]\OT1/cmtt/m/n/10 HSHNRNPA        2404 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC
AAAGCAAGAG[] 

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[]\OT1/cmtt/m/n/10 HSHNCPA1        231  ATGGCTAGTGCTTCATCCAGCCAAAGAG           
  GTCGAAGT[] 

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[]                     \OT1/cmtt/m/n/10 ATGGCTAGTGCTTCATCCAGCCAAAGAG           
  GTCGAAGT[] 

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[]\OT1/cmtt/m/n/10 HSHNRNPA        2453 ATGGCTAGTGCTTCATCCAGCCAAAGAG<-2481:2566
->GTCGAAGT[] 

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[]\OT1/cmtt/m/n/10 HSHNCPA1        267  GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC
GGTGGGAATG[] 

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[]                     \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 (69.74638pt too wide) in paragraph at lines 2255--2255
[]\OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s",te
mp->baseseq->name);[] 

Overfull \hbox (59.24648pt too wide) in paragraph at lines 2255--2255
[]      \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,
mat,-12,-2,NULL);[] 

Overfull \hbox (95.99615pt too wide) in paragraph at lines 2255--2255
[]\OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query->na
me,temp->baseseq->name);[] 

Overfull \hbox (6.74693pt too wide) in paragraph at lines 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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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 dynamite.pdf (62 pages, 214458 bytes).
Transcript written on dynamite.log.
cd docs && pdflatex dynamite.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.21 (TeX Live 2020/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./dynamite.tex
LaTeX2e <2020-10-01> patch level 4
L3 programming layer <2021-01-09> xparse <2020-03-03>
(/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 2020/04/10 v1.4m 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))"[] 

Overfull \hbox (59.24648pt too wide) in paragraph at lines 1967--1967
[]        \OT1/cmtt/m/n/10 For function CDNA\_BASE, you have arguments j and qu
ery, which do not[] 

Overfull \hbox (11.99689pt too wide) in paragraph at lines 1967--1967
[]\OT1/cmtt/m/n/10 expect to paired directly in a function. This is just a warn
ing that[] 
[45]
Overfull \hbox (17.24684pt too wide) in paragraph at lines 2014--2014
[]  \OT1/cmtt/m/n/10 throw_warning("Letter %c does not exist in comparison matr
ix",one);[] 

Overfull \hbox (17.24684pt too wide) in paragraph at lines 2014--2014
[]  \OT1/cmtt/m/n/10 throw_warning("Letter %c does not exist in comparison matr
ix",two);[] 
[46] [47]
Overfull \hbox (74.99634pt too wide) in paragraph at lines 2255--2255
[]  \OT1/cmtt/m/n/10 fprintf(stdout,"dbsearch [options] <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[] 
[48]
Overfull \hbox (43.49661pt too wide) in paragraph at lines 2255--2255
[]   \OT1/cmtt/m/n/10 * care about which implementation is used, and does not k
now either (!)[] 
[49]
Overfull \hbox (106.49606pt too wide) in paragraph at lines 2255--2255
[]  \OT1/cmtt/m/n/10 /* 10 means a score cutoff of 10, -1 means don't report on
 stderr search progress */[] 

Overfull \hbox (32.9967pt too wide) in paragraph at lines 2255--2255
[]  \OT1/cmtt/m/n/10 if( search_ProteinSW(dbsi,out,querydb,prodb,mat,-12,-2) !=
 SEARCH_OK )[] 

Overfull \hbox (53.99652pt too wide) in paragraph at lines 2255--2255
[]    \OT1/cmtt/m/n/10 fatal("Some sort of error in the database search. Dieing
 ungracefully");[] 

Overfull \hbox (48.74657pt too wide) in paragraph at lines 2255--2255
[]    \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s
",query->name);[] 

Overfull \hbox (174.74547pt too wide) in paragraph at lines 2255--2255
[]      \OT1/cmtt/m/n/10 fprintf(stdout,"Comparison to %s was %d score\n",out->
ds[i]->target->name,out->ds[i]->score);[] 

Overfull \hbox (1.49698pt too wide) in paragraph at lines 2255--2255
[]      \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta
rget);[] 
[50]
Overfull \hbox (69.74638pt too wide) in paragraph at lines 2255--2255
[]\OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s",te
mp->baseseq->name);[] 

Overfull \hbox (59.24648pt too wide) in paragraph at lines 2255--2255
[]      \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,
mat,-12,-2,NULL);[] 

Overfull \hbox (95.99615pt too wide) in paragraph at lines 2255--2255
[]\OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query->na
me,temp->baseseq->name);[] 

Overfull \hbox (6.74693pt too wide) in paragraph at lines 2255--2255
[]      \OT1/cmtt/m/n/10 write_pretty_seq_align(alb,query,temp->baseseq,15,50,s
tdout);[] 

Overfull \hbox (32.9967pt too wide) in paragraph at lines 2263--2263
[]  \OT1/cmtt/m/n/10 if( search_ProteinSW(dbsi,out,querydb,prodb,mat,-12,-2) !=
 SEARCH_OK )[] 

Overfull \hbox (53.99652pt too wide) in paragraph at lines 2263--2263
[]    \OT1/cmtt/m/n/10 fatal("Some sort of error in the database search. Dieing
 ungracefully");[] 
[51]
Overfull \hbox (1.49698pt too wide) in paragraph at lines 2292--2292
[]      \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta
rget);[] 
[52] [53] [54] [55] [56]
Overfull \hbox (1.32472pt too wide) in paragraph at lines 2528--2534
\OT1/cmr/m/n/10 de-scribed by a "state...endstate" multi-line block. Within eac
h "state...endstate"
[57] [58] [59] [60] [61]
Overfull \hbox (1.75064pt too wide) in paragraph at lines 2772--2776
\OT1/cmr/m/n/10 Dy-na-mite file: for ex-am-ple the fol-low-ing er-ror was made 
by mistyp-ing ``MATCH''

Overfull \hbox (59.24648pt too wide) in paragraph at lines 2792--2792
[]        \OT1/cmtt/m/n/10 In matrix ProteinSW - State MATCH asks for source MA
TCH2 but there is[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 2792--2792
[]        \OT1/cmtt/m/n/10 Failing simple cross-checks, aborting before calc-li
ne parsing[] 
[62] [63] [64] (./dynamite.aux)

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10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr12.pfb>
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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 dynamite.pdf (64 pages, 218023 bytes).
Transcript written on dynamite.log.
cd docs && pdflatex wise2.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.21 (TeX Live 2020/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./wise2.tex
LaTeX2e <2020-10-01> patch level 4
L3 programming layer <2021-01-09> xparse <2020-03-03>
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2020/04/10 v1.4m Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def)
No file wise2.aux.
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]
No file wise2.toc.
[2] [3] [4]

LaTeX Warning: Reference `genewise_large' on page 5 undefined on input line 110
.


LaTeX Warning: Reference `estwise_large' on page 5 undefined on input line 113.



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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[] 

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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
IMTDRGSGKK[] 

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[]\OT1/cmtt/m/n/10 HSHNRNPA        2093 acggctagaaatgggaaggaggcccagttgctgaaggag
aaagcgagaa[] 

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[]                     \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[] 

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[]\OT1/cmtt/m/n/10 HSHNRNPA        2240 agtgtgatggcgtggaagAGTAAGTA  Intron 3   
TAGTTcatca[] 

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[]                     \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]

LaTeX Warning: Reference `sec:start_end' on page 9 undefined on input line 297.


[9]

LaTeX Warning: Reference `half_and_blast' on page 10 undefined on input line 34
6.

[10] [11]

LaTeX Warning: Reference `genewise_large' on page 12 undefined on input line 45
5.


LaTeX Warning: Reference `estwise_large' on page 12 undefined on input line 455
.


LaTeX Warning: Reference `compile_pthread' on page 12 undefined on input line 4
66.


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3.

[12]

LaTeX Warning: Reference `half_and_blast' on page 13 undefined on input line 51
3.

[13] [14]

LaTeX Warning: Reference `running_pthread' on page 15 undefined on input line 6
13.

[15] [16] [17]

LaTeX Warning: Reference `Figure:genewise21' on page 18 undefined on input line
 708.

[18] [19] [20]

LaTeX Warning: Reference `Figure:genewise623' on page 21 undefined on input lin
e 900.

[21]
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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]
Overfull \hbox (68.08423pt too wide) in paragraph at lines 1108--1109
[]\OT1/cmr/m/n/10 The half-wise pro-tein database, found at ftp://ftp.sanger.ac
.uk/pub/birney/wise2/halfwise 
[26]

LaTeX Warning: Reference `sec:commonmode' on page 27 undefined on input line 11
81.

[27]

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0.

[28]
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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]

LaTeX Warning: Reference `sec:alg' on page 30 undefined on input line 1276.


Overfull \hbox (36.99692pt too wide) in paragraph at lines 1312--1312
 []\OT1/cmtt/m/n/10 Bits   Query         start end Target      start end   idel
s introns[] 

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

LaTeX Warning: Reference `sec:start_end' on page 32 undefined on input line 137
7.

[32] [33] [34]

LaTeX Warning: Reference `sec:start_end' on page 35 undefined on input line 146
9.

[35] [36]

LaTeX Warning: Reference `compile_pthread' on page 37 undefined on input line 1
561.

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

LaTeX Warning: There were undefined references.


LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.

 )
(see the transcript file for additional information) </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 (42 pages, 206333 bytes).
Transcript written on wise2.log.
cd docs && pdflatex wise2.tex
This is pdfTeX, Version 3.14159265-2.6-1.40.21 (TeX Live 2020/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./wise2.tex
LaTeX2e <2020-10-01> patch level 4
L3 programming layer <2021-01-09> xparse <2020-03-03>
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2020/04/10 v1.4m Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def)
(./wise2.aux)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./wise2.toc [2])
[3] [4] [5]
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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]
Overfull \hbox (32.9967pt too wide) in paragraph at lines 206--206
[]\OT1/cmtt/m/n/10 Warning: The bits scores is not probablistically correct for
 single seqs[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206
[]\OT1/cmtt/m/n/10 roa1_drome        88 AQKSRPHKIDGRVVEPKRAVPRQ                
       DID[] 

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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[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206
[]\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[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 206--206
[]\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
IMTDRGSGKK[] 

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[]\OT1/cmtt/m/n/10 HSHNRNPA        2093 acggctagaaatgggaaggaggcccagttgctgaaggag
aaagcgagaa[] 

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[]                     \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[] 
[7]
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[]                     \OT1/cmtt/m/n/10 RGFAFVTFDDHDSVDKIV          L:I[att]   
     QKYHT[] 

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[]\OT1/cmtt/m/n/10 HSHNRNPA        2240 agtgtgatggcgtggaagAGTAAGTA  Intron 3   
TAGTTcatca[] 

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[]                     \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][] 
[8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18]

LaTeX Warning: Reference `Figure:genewise21' on page 19 undefined on input line
 708.

[19] [20] [21] [22]
Overfull \hbox (2.03789pt too wide) in paragraph at lines 965--968
[]\OT1/cmr/m/n/10 Algorithms are named in two parts, \OT1/cmr/m/it/10 descripti
ve-word state-number:transition-
[23] [24] [25] [26]
Overfull \hbox (68.08423pt too wide) in paragraph at lines 1108--1109
[]\OT1/cmr/m/n/10 The half-wise pro-tein database, found at ftp://ftp.sanger.ac
.uk/pub/birney/wise2/halfwise 
[27] [28] [29]
Overfull \hbox (42.24687pt too wide) in paragraph at lines 1268--1268
 []\OT1/cmtt/m/n/10 pexon <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, 208648 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 -d debian/wise/usr/bin
   dh_install -a
	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/
	install -d debian/.debhelper/generated/wise
	install -d debian/.debhelper/generated/wise-doc
	install -d debian/.debhelper/generated/wise-data
   dh_installdocs -a
	install -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 -p -m0644 debian/changelog debian/wise/usr/share/doc/wise/changelog.Debian
   dh_installexamples -a
   dh_installman -a
	install -d debian/wise/usr/share/man/man1/
	install -p -m0644 ./debian/manpages.d/dba.1 debian/wise/usr/share/man/man1/dba.1
	install -p -m0644 ./debian/manpages.d/dnal.1 debian/wise/usr/share/man/man1/dnal.1
	install -p -m0644 ./debian/manpages.d/estwise.1 debian/wise/usr/share/man/man1/estwise.1
	install -p -m0644 ./debian/manpages.d/estwisedb.1 debian/wise/usr/share/man/man1/estwisedb.1
	install -p -m0644 ./debian/manpages.d/genewise.1 debian/wise/usr/share/man/man1/genewise.1
	install -p -m0644 ./debian/manpages.d/genewisedb.1 debian/wise/usr/share/man/man1/genewisedb.1
	install -p -m0644 ./debian/manpages.d/genomewise.1 debian/wise/usr/share/man/man1/genomewise.1
	install -p -m0644 ./debian/manpages.d/promoterwise.1 debian/wise/usr/share/man/man1/promoterwise.1
	install -p -m0644 ./debian/manpages.d/psw.1 debian/wise/usr/share/man/man1/psw.1
	install -p -m0644 ./debian/manpages.d/pswdb.1 debian/wise/usr/share/man/man1/pswdb.1
	install -p -m0644 ./debian/manpages.d/scanwise.1 debian/wise/usr/share/man/man1/scanwise.1
	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 -d debian/wise/usr/lib/debug/.dwz/x86_64-linux-gnu
	dwz -mdebian/wise/usr/lib/debug/.dwz/x86_64-linux-gnu/wise.debug -M/usr/lib/debug/.dwz/x86_64-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
	x86_64-linux-gnu-objcopy --compress-debug-sections debian/wise/usr/lib/debug/.dwz/x86_64-linux-gnu/wise.debug
   dh_strip -a
	install -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/75
	x86_64-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/75/fd346f8b0a646b3b639a9af34248c6c7e740eb.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/75/fd346f8b0a646b3b639a9af34248c6c7e740eb.debug
	x86_64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/scanwise_server
	x86_64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/75/fd346f8b0a646b3b639a9af34248c6c7e740eb.debug debian/wise/usr/bin/scanwise_server
	install -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/27
	x86_64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/psw debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/27/801f228eaacb6f6eab1cccae2dab973c26075d.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/27/801f228eaacb6f6eab1cccae2dab973c26075d.debug
	x86_64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/psw
	x86_64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/27/801f228eaacb6f6eab1cccae2dab973c26075d.debug debian/wise/usr/bin/psw
	install -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/26
	x86_64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genewisedb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/26/af25f300dbd9fc5280b69bed6bf60f742bb5e3.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/26/af25f300dbd9fc5280b69bed6bf60f742bb5e3.debug
	x86_64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genewisedb
	x86_64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/26/af25f300dbd9fc5280b69bed6bf60f742bb5e3.debug debian/wise/usr/bin/genewisedb
	install -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fd
	x86_64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/pswdb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fd/c6b3cd08da6696781f7d9609199b0f3bc4acf8.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fd/c6b3cd08da6696781f7d9609199b0f3bc4acf8.debug
	x86_64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/pswdb
	x86_64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/fd/c6b3cd08da6696781f7d9609199b0f3bc4acf8.debug debian/wise/usr/bin/pswdb
	install -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a3
	x86_64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genewise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a3/34ac9f4934f631fc78f68cfbe9a6e5a9d7b64a.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a3/34ac9f4934f631fc78f68cfbe9a6e5a9d7b64a.debug
	x86_64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genewise
	x86_64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a3/34ac9f4934f631fc78f68cfbe9a6e5a9d7b64a.debug debian/wise/usr/bin/genewise
	install -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/95
	x86_64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/estwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/95/834f86eeb695ee1d7457279f5715e03f086896.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/95/834f86eeb695ee1d7457279f5715e03f086896.debug
	x86_64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/estwise
	x86_64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/95/834f86eeb695ee1d7457279f5715e03f086896.debug debian/wise/usr/bin/estwise
	install -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/61
	x86_64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/estwisedb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/61/aab8b496727f6c24e9e9a43968c30b89a4922f.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/61/aab8b496727f6c24e9e9a43968c30b89a4922f.debug
	x86_64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/estwisedb
	x86_64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/61/aab8b496727f6c24e9e9a43968c30b89a4922f.debug debian/wise/usr/bin/estwisedb
	install -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e1
	x86_64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/promoterwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e1/c76040377973befe39043eccf7d8305a13fc60.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e1/c76040377973befe39043eccf7d8305a13fc60.debug
	x86_64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/promoterwise
	x86_64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e1/c76040377973befe39043eccf7d8305a13fc60.debug debian/wise/usr/bin/promoterwise
	install -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/11
	x86_64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/dnal debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/11/5a726caab2a998d28241702ca9be92b714ded8.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/11/5a726caab2a998d28241702ca9be92b714ded8.debug
	x86_64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/dnal
	x86_64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/11/5a726caab2a998d28241702ca9be92b714ded8.debug debian/wise/usr/bin/dnal
	install -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/30
	x86_64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genomewise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/30/df5fa30f83bfde2e40b175c8437a217fa573ed.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/30/df5fa30f83bfde2e40b175c8437a217fa573ed.debug
	x86_64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genomewise
	x86_64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/30/df5fa30f83bfde2e40b175c8437a217fa573ed.debug debian/wise/usr/bin/genomewise
	install -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/87
	x86_64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/dba debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/87/f4876551fbd2d4e816ae1fa57599dcc750cab7.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/87/f4876551fbd2d4e816ae1fa57599dcc750cab7.debug
	x86_64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/dba
	x86_64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/87/f4876551fbd2d4e816ae1fa57599dcc750cab7.debug debian/wise/usr/bin/dba
	install -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/92
	x86_64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/scanwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/92/6875fb149f3c94f9b675277914ac4debf823b2.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/92/6875fb149f3c94f9b675277914ac4debf823b2.debug
	x86_64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/scanwise
	x86_64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/92/6875fb149f3c94f9b675277914ac4debf823b2.debug debian/wise/usr/bin/scanwise
	install -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.dwz
	cp --reflink=auto -a debian/wise/usr/lib/debug/.dwz/x86_64-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 -d debian/.debhelper/wise/dbgsym-root/usr/share/doc
	ln -s wise debian/.debhelper/wise/dbgsym-root/usr/share/doc/wise-dbgsym
   dh_makeshlibs -a
	rm -f debian/wise/DEBIAN/shlibs
   dh_shlibdeps -a
	install -d debian/wise/DEBIAN
	dpkg-shlibdeps -Tdebian/wise.substvars debian/wise/usr/bin/scanwise_server debian/wise/usr/bin/psw debian/wise/usr/bin/genewisedb debian/wise/usr/bin/pswdb debian/wise/usr/bin/genewise debian/wise/usr/bin/estwise debian/wise/usr/bin/estwisedb debian/wise/usr/bin/promoterwise debian/wise/usr/bin/dnal debian/wise/usr/bin/genomewise debian/wise/usr/bin/dba debian/wise/usr/bin/scanwise
   dh_installdeb -a
   dh_gencontrol -a
	echo misc:Depends= >> debian/wise.substvars
	echo misc:Pre-Depends= >> debian/wise.substvars
	install -d debian/.debhelper/wise/dbgsym-root/DEBIAN
	dpkg-gencontrol -pwise -ldebian/changelog -Tdebian/wise.substvars -Pdebian/.debhelper/wise/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=wise-dbgsym "-DDepends=wise (= \${binary:Version})" "-DDescription=debug symbols for wise" "-DBuild-Ids=115a726caab2a998d28241702ca9be92b714ded8 26af25f300dbd9fc5280b69bed6bf60f742bb5e3 27801f228eaacb6f6eab1cccae2dab973c26075d 30df5fa30f83bfde2e40b175c8437a217fa573ed 61aab8b496727f6c24e9e9a43968c30b89a4922f 75fd346f8b0a646b3b639a9af34248c6c7e740eb 87f4876551fbd2d4e816ae1fa57599dcc750cab7 926875fb149f3c94f9b675277914ac4debf823b2 95834f86eeb695ee1d7457279f5715e03f086896 a334ac9f4934f631fc78f68cfbe9a6e5a9d7b64a e1c76040377973befe39043eccf7d8305a13fc60 fdc6b3cd08da6696781f7d9609199b0f3bc4acf8" -DSection=debug -UMulti-Arch -UReplaces -UBreaks
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/DEBIAN/control
	dpkg-gencontrol -pwise -ldebian/changelog -Tdebian/wise.substvars -Pdebian/wise
	chmod 0644 -- debian/wise/DEBIAN/control
   dh_md5sums -a
	cd debian/wise >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	chmod 0644 -- debian/wise/DEBIAN/md5sums
	cd debian/.debhelper/wise/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/DEBIAN/md5sums
   dh_builddeb -a
	dpkg-deb --root-owner-group --build debian/wise ..
dpkg-deb: building package 'wise' in '../wise_2.4.1-23_amd64.deb'.
	dpkg-deb --root-owner-group --build debian/.debhelper/wise/dbgsym-root ..
dpkg-deb: building package 'wise-dbgsym' in '../wise-dbgsym_2.4.1-23_amd64.deb'.
 dpkg-genbuildinfo --build=any
 dpkg-genchanges --build=any >../wise_2.4.1-23_amd64.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 2021-07-17T08:20:38Z

Finished
--------

I: Built successfully

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


wise_2.4.1-23_amd64.changes:
----------------------------

Format: 1.8
Date: Sat, 18 Apr 2020 17:57:01 +0200
Source: wise
Binary: wise wise-dbgsym
Built-For-Profiles: cross nocheck
Architecture: amd64
Version: 2.4.1-23
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Helmut Grohne <helmut@subdivi.de>
Description:
 wise       - comparison of biopolymers, like DNA and protein sequences
Closes: 958094
Changes:
 wise (2.4.1-23) unstable; urgency=medium
 .
   * Team upload.
   * Do not hard code the build architecture pkg-config
     Closes: #958094
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Files:
 ca5789da492b0d615176d0208e1de17d 8137328 debug optional wise-dbgsym_2.4.1-23_amd64.deb
 fcd4f74b0b8270b3159a48b6ac705c9b 8629 science optional wise_2.4.1-23_amd64.buildinfo
 a4276fa712b8bdf192b0d4ce700396f8 1036224 science optional wise_2.4.1-23_amd64.deb

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

Format: 1.0
Source: wise
Binary: wise wise-dbgsym
Architecture: amd64
Version: 2.4.1-23
Checksums-Md5:
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Checksums-Sha256:
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 cba65c4ae51ff48e4f9f74b39b51fdb231a925cfb1ba204cfd8bb2e3ee707e1b 1036224 wise_2.4.1-23_amd64.deb
Build-Origin: Debian
Build-Architecture: arm64
Build-Date: Sat, 17 Jul 2021 08:20:36 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
 autoconf (= 2.69-14),
 automake (= 1:1.16.3-2),
 autopoint (= 0.21-4),
 autotools-dev (= 20180224.1+nmu1),
 base-files (= 11.1),
 base-passwd (= 3.5.51),
 bash (= 5.1-3),
 binutils (= 2.35.2-2),
 binutils-aarch64-linux-gnu (= 2.35.2-2),
 binutils-common (= 2.35.2-2),
 bsdextrautils (= 2.36.1-7),
 bsdutils (= 1:2.36.1-7),
 build-essential (= 12.9),
 bzip2 (= 1.0.8-4),
 coreutils (= 8.32-4),
 cpp (= 4:10.2.1-1),
 cpp-10 (= 10.2.1-6),
 dash (= 0.5.11+git20210120+802ebd4-1),
 debconf (= 1.5.77),
 debhelper (= 13.3.4),
 debianutils (= 4.11.2),
 dh-autoreconf (= 20),
 dh-strip-nondeterminism (= 1.12.0-1),
 diffutils (= 1:3.7-5),
 docbook (= 4.5-6),
 docbook-to-man (= 1:2.0.0-45),
 dpkg (= 1.20.9),
 dpkg-dev (= 1.20.9),
 dwz (= 0.14-1),
 file (= 1:5.39-3),
 findutils (= 4.8.0-1),
 fontconfig-config (= 2.13.1-4.2),
 fonts-dejavu-core (= 2.37-2),
 fonts-lmodern (= 2.004.5-6.1),
 fonts-urw-base35 (= 20200910-1),
 g++ (= 4:10.2.1-1),
 g++-10 (= 10.2.1-6),
 gcc (= 4:10.2.1-1),
 gcc-10 (= 10.2.1-6),
 gcc-10-base (= 10.2.1-6),
 gettext (= 0.21-4),
 gettext-base (= 0.21-4),
 ghostscript (= 9.53.3~dfsg-7),
 grep (= 3.6-1),
 groff-base (= 1.22.4-6),
 gzip (= 1.10-4),
 hevea (= 2.34-2+b1),
 hostname (= 3.23),
 init-system-helpers (= 1.60),
 intltool-debian (= 0.35.0+20060710.5),
 libacl1 (= 2.2.53-10),
 libarchive-zip-perl (= 1.68-1),
 libasan6 (= 10.2.1-6),
 libatomic1 (= 10.2.1-6),
 libattr1 (= 1:2.4.48-6),
 libaudit-common (= 1:3.0-2),
 libaudit1 (= 1:3.0-2),
 libavahi-client3 (= 0.8-5),
 libavahi-common-data (= 0.8-5),
 libavahi-common3 (= 0.8-5),
 libbinutils (= 2.35.2-2),
 libblkid-dev (= 2.36.1-7),
 libblkid1 (= 2.36.1-7),
 libbrotli1 (= 1.0.9-2+b2),
 libbsd0 (= 0.11.3-1),
 libbz2-1.0 (= 1.0.8-4),
 libc-bin (= 2.31-13),
 libc-dev-bin (= 2.31-13),
 libc6 (= 2.31-13),
 libc6-dev (= 2.31-13),
 libcairo2 (= 1.16.0-5),
 libcap-ng0 (= 0.7.9-2.2+b1),
 libcc1-0 (= 10.2.1-6),
 libcom-err2 (= 1.46.2-2),
 libcrypt-dev (= 1:4.4.18-4),
 libcrypt1 (= 1:4.4.18-4),
 libctf-nobfd0 (= 2.35.2-2),
 libctf0 (= 2.35.2-2),
 libcups2 (= 2.3.3op2-3+deb11u1),
 libdatrie1 (= 0.2.13-1),
 libdb5.3 (= 5.3.28+dfsg1-0.8),
 libdbus-1-3 (= 1.12.20-2),
 libdebconfclient0 (= 0.260),
 libdebhelper-perl (= 13.3.4),
 libdeflate0 (= 1.7-1),
 libdpkg-perl (= 1.20.9),
 libelf1 (= 0.183-3),
 libexpat1 (= 2.2.10-2),
 libffi-dev (= 3.3-6),
 libffi7 (= 3.3-6),
 libfile-stripnondeterminism-perl (= 1.12.0-1),
 libfontconfig1 (= 2.13.1-4.2),
 libfontenc1 (= 1:1.1.4-1),
 libfreetype6 (= 2.10.4+dfsg-1),
 libgcc-10-dev (= 10.2.1-6),
 libgcc-s1 (= 10.2.1-6),
 libgcrypt20 (= 1.8.7-6),
 libgdbm-compat4 (= 1.19-2),
 libgdbm6 (= 1.19-2),
 libglib2.0-0 (= 2.66.8-1),
 libglib2.0-bin (= 2.66.8-1),
 libglib2.0-data (= 2.66.8-1),
 libglib2.0-dev (= 2.66.8-1),
 libglib2.0-dev-bin (= 2.66.8-1),
 libgmp10 (= 2:6.2.1+dfsg-1),
 libgnutls30 (= 3.7.1-5),
 libgomp1 (= 10.2.1-6),
 libgpg-error0 (= 1.38-2),
 libgraphite2-3 (= 1.3.14-1),
 libgs9 (= 9.53.3~dfsg-7),
 libgs9-common (= 9.53.3~dfsg-7),
 libgssapi-krb5-2 (= 1.18.3-5),
 libharfbuzz0b (= 2.7.4-1),
 libhogweed6 (= 3.7.3-1),
 libice6 (= 2:1.0.10-1),
 libicu67 (= 67.1-7),
 libidn11 (= 1.33-3),
 libidn2-0 (= 2.3.0-5),
 libijs-0.35 (= 0.35-15),
 libisl23 (= 0.23-1),
 libitm1 (= 10.2.1-6),
 libjbig0 (= 2.1-3.1+b2),
 libjbig2dec0 (= 0.19-3),
 libjpeg62-turbo (= 1:2.0.6-4),
 libjs-jquery (= 3.5.1+dfsg+~3.5.5-7),
 libk5crypto3 (= 1.18.3-5),
 libkeyutils1 (= 1.6.1-2),
 libkpathsea6 (= 2020.20200327.54578-7),
 libkrb5-3 (= 1.18.3-5),
 libkrb5support0 (= 1.18.3-5),
 liblcms2-2 (= 2.12~rc1-2),
 liblsan0 (= 10.2.1-6),
 liblz4-1 (= 1.9.3-2),
 liblzma5 (= 5.2.5-2),
 libmagic-mgc (= 1:5.39-3),
 libmagic1 (= 1:5.39-3),
 libmd0 (= 1.0.3-3),
 libmime-charset-perl (= 1.012.2-1),
 libmount-dev (= 2.36.1-7),
 libmount1 (= 2.36.1-7),
 libmpc3 (= 1.2.0-1),
 libmpdec3 (= 2.5.1-2),
 libmpfr6 (= 4.1.0-3),
 libncursesw6 (= 6.2+20201114-2),
 libnetpbm10 (= 2:10.0-15.4),
 libnettle8 (= 3.7.3-1),
 libnsl-dev (= 1.3.0-2),
 libnsl2 (= 1.3.0-2),
 libopenjp2-7 (= 2.4.0-3),
 libosp5 (= 1.5.2-13+b2),
 libp11-kit0 (= 0.23.22-1),
 libpam-modules (= 1.4.0-9),
 libpam-modules-bin (= 1.4.0-9),
 libpam-runtime (= 1.4.0-9),
 libpam0g (= 1.4.0-9),
 libpaper-utils (= 1.1.28+b1),
 libpaper1 (= 1.1.28+b1),
 libpcre16-3 (= 2:8.39-13),
 libpcre2-16-0 (= 10.36-2),
 libpcre2-32-0 (= 10.36-2),
 libpcre2-8-0 (= 10.36-2),
 libpcre2-dev (= 10.36-2),
 libpcre2-posix2 (= 10.36-2),
 libpcre3 (= 2:8.39-13),
 libpcre3-dev (= 2:8.39-13),
 libpcre32-3 (= 2:8.39-13),
 libpcrecpp0v5 (= 2:8.39-13),
 libperl5.32 (= 5.32.1-4),
 libpipeline1 (= 1.5.3-1),
 libpixman-1-0 (= 0.40.0-1),
 libpng16-16 (= 1.6.37-3),
 libptexenc1 (= 2020.20200327.54578-7),
 libpython3-stdlib (= 3.9.2-3),
 libpython3.9-minimal (= 3.9.2-1),
 libpython3.9-stdlib (= 3.9.2-1),
 libquadmath0 (= 10.2.1-6),
 libreadline8 (= 8.1-2),
 libseccomp2 (= 2.5.1-1),
 libselinux1 (= 3.1-3),
 libselinux1-dev (= 3.1-3),
 libsepol1 (= 3.1-1),
 libsepol1-dev (= 3.1-1),
 libsigsegv2 (= 2.13-1),
 libsm6 (= 2:1.2.3-1),
 libsmartcols1 (= 2.36.1-7),
 libsombok3 (= 2.4.0-2+b1),
 libsqlite3-0 (= 3.34.1-3),
 libssl1.1 (= 1.1.1k-1),
 libstdc++-10-dev (= 10.2.1-6),
 libstdc++6 (= 10.2.1-6),
 libsub-override-perl (= 0.09-2),
 libsynctex2 (= 2020.20200327.54578-7),
 libsystemd0 (= 247.3-5),
 libtasn1-6 (= 4.16.0-2),
 libteckit0 (= 2.5.10+ds1-3),
 libtexlua53 (= 2020.20200327.54578-7),
 libthai-data (= 0.1.28-4),
 libthai0 (= 0.1.28-4),
 libtiff5 (= 4.2.0-1),
 libtinfo6 (= 6.2+20201114-2),
 libtirpc-common (= 1.3.1-1),
 libtirpc-dev (= 1.3.1-1),
 libtirpc3 (= 1.3.1-1),
 libtool (= 2.4.6-15),
 libtsan0 (= 10.2.1-6),
 libubsan1 (= 10.2.1-6),
 libuchardet0 (= 0.0.7-1),
 libudev1 (= 247.3-5),
 libunicode-linebreak-perl (= 0.0.20190101-1+b2),
 libunistring2 (= 0.9.10-4),
 libuuid1 (= 2.36.1-7),
 libwebp6 (= 0.6.1-2.1),
 libx11-6 (= 2:1.7.1-1),
 libx11-data (= 2:1.7.1-1),
 libxau6 (= 1:1.0.9-1),
 libxaw7 (= 2:1.0.13-1.1),
 libxcb-render0 (= 1.14-3),
 libxcb-shm0 (= 1.14-3),
 libxcb1 (= 1.14-3),
 libxdmcp6 (= 1:1.1.2-3),
 libxext6 (= 2:1.3.3-1.1),
 libxi6 (= 2:1.7.10-1),
 libxml2 (= 2.9.10+dfsg-6.7),
 libxmu6 (= 2:1.1.2-2+b3),
 libxpm4 (= 1:3.5.12-1),
 libxrender1 (= 1:0.9.10-1),
 libxt6 (= 1:1.2.0-1),
 libzstd1 (= 1.4.8+dfsg-2.1),
 libzzip-0-13 (= 0.13.72+dfsg.1-1.1),
 linux-libc-dev (= 5.10.46-1),
 lmodern (= 2.004.5-6.1),
 login (= 1:4.8.1-1),
 lsb-base (= 11.1.0),
 m4 (= 1.4.18-5),
 make (= 4.3-4.1),
 man-db (= 2.9.4-2),
 mawk (= 1.3.4.20200120-2),
 media-types (= 4.0.0),
 ncurses-base (= 6.2+20201114-2),
 ncurses-bin (= 6.2+20201114-2),
 netpbm (= 2:10.0-15.4),
 opensp (= 1.5.2-13+b2),
 patch (= 2.7.6-7),
 perl (= 5.32.1-4),
 perl-base (= 5.32.1-4),
 perl-modules-5.32 (= 5.32.1-4),
 pkg-config (= 0.29.2-1),
 po-debconf (= 1.0.21+nmu1),
 poppler-data (= 0.4.10-1),
 python3 (= 3.9.2-3),
 python3-distutils (= 3.9.2-1),
 python3-lib2to3 (= 3.9.2-1),
 python3-minimal (= 3.9.2-3),
 python3.9 (= 3.9.2-1),
 python3.9-minimal (= 3.9.2-1),
 readline-common (= 8.1-2),
 sed (= 4.7-1),
 sensible-utils (= 0.0.14),
 sgml-base (= 1.30),
 sgml-data (= 2.0.11+nmu1),
 sysvinit-utils (= 2.96-7),
 t1utils (= 1.41-4),
 tar (= 1.34+dfsg-1),
 tex-common (= 6.16),
 texlive-base (= 2020.20210202-3),
 texlive-binaries (= 2020.20200327.54578-7),
 texlive-extra-utils (= 2020.20210202-3),
 texlive-latex-base (= 2020.20210202-3),
 texlive-luatex (= 2020.20210202-3),
 texlive-plain-generic (= 2020.20210202-3),
 tzdata (= 2021a-1),
 ucf (= 3.0043),
 util-linux (= 2.36.1-7),
 uuid-dev (= 2.36.1-7),
 x11-common (= 1:7.7+22),
 xdg-utils (= 1.1.3-4.1),
 xfonts-encodings (= 1:1.0.4-2.1),
 xfonts-utils (= 1:7.7+6),
 xml-core (= 0.18+nmu1),
 xz-utils (= 5.2.5-2),
 zlib1g (= 1:1.2.11.dfsg-2),
 zlib1g-dev (= 1:1.2.11.dfsg-2)
Environment:
 DEB_BUILD_OPTIONS="nocheck parallel=1"
 DEB_BUILD_PROFILES="cross nocheck"
 LANG="en_GB.UTF-8"
 LC_ALL="C.UTF-8"
 SOURCE_DATE_EPOCH="1587225421"


+------------------------------------------------------------------------------+
| Package contents                                                             |
+------------------------------------------------------------------------------+


wise-dbgsym_2.4.1-23_amd64.deb
------------------------------

 new Debian package, version 2.0.
 size 8137328 bytes: control archive=1132 bytes.
     812 bytes,    12 lines      control              
    1353 bytes,    13 lines      md5sums              
 Package: wise-dbgsym
 Source: wise
 Version: 2.4.1-23
 Auto-Built-Package: debug-symbols
 Architecture: amd64
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 9385
 Depends: wise (= 2.4.1-23)
 Section: debug
 Priority: optional
 Description: debug symbols for wise
 Build-Ids: 115a726caab2a998d28241702ca9be92b714ded8 26af25f300dbd9fc5280b69bed6bf60f742bb5e3 27801f228eaacb6f6eab1cccae2dab973c26075d 30df5fa30f83bfde2e40b175c8437a217fa573ed 61aab8b496727f6c24e9e9a43968c30b89a4922f 75fd346f8b0a646b3b639a9af34248c6c7e740eb 87f4876551fbd2d4e816ae1fa57599dcc750cab7 926875fb149f3c94f9b675277914ac4debf823b2 95834f86eeb695ee1d7457279f5715e03f086896 a334ac9f4934f631fc78f68cfbe9a6e5a9d7b64a e1c76040377973befe39043eccf7d8305a13fc60 fdc6b3cd08da6696781f7d9609199b0f3bc4acf8

drwxr-xr-x root/root         0 2020-04-18 15:57 ./
drwxr-xr-x root/root         0 2020-04-18 15:57 ./usr/
drwxr-xr-x root/root         0 2020-04-18 15:57 ./usr/lib/
drwxr-xr-x root/root         0 2020-04-18 15:57 ./usr/lib/debug/
drwxr-xr-x root/root         0 2020-04-18 15:57 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2020-04-18 15:57 ./usr/lib/debug/.build-id/11/
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drwxr-xr-x root/root         0 2020-04-18 15:57 ./usr/lib/debug/.build-id/75/
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-rw-r--r-- root/root     92128 2020-04-18 15:57 ./usr/lib/debug/.dwz/x86_64-linux-gnu/wise.debug
drwxr-xr-x root/root         0 2020-04-18 15:57 ./usr/share/
drwxr-xr-x root/root         0 2020-04-18 15:57 ./usr/share/doc/
lrwxrwxrwx root/root         0 2020-04-18 15:57 ./usr/share/doc/wise-dbgsym -> wise


wise_2.4.1-23_amd64.deb
-----------------------

 new Debian package, version 2.0.
 size 1036224 bytes: control archive=1960 bytes.
    1720 bytes,    33 lines      control              
    1742 bytes,    29 lines      md5sums              
 Package: wise
 Version: 2.4.1-23
 Architecture: amd64
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 9942
 Depends: libc6 (>= 2.29), libglib2.0-0 (>= 2.12.0), wise-data (= 2.4.1-23)
 Suggests: wise-doc (= 2.4.1-23)
 Section: science
 Priority: optional
 Homepage: https://www.ebi.ac.uk/~birney/wise2/
 Description: comparison of biopolymers, like DNA and protein sequences
  Wise2 is a package focused on comparisons of biopolymers, commonly DNA
  and protein sequences. There are many other packages which do
  this, probably the best known being BLAST package (from NCBI) and the
  Fasta package (from Bill Pearson). There are other packages, such as
  the HMMER package (Sean Eddy) or SAM package (UC Santa Cruz) focused
  on hidden Markov models (HMMs) of biopolymers.
  .
  Wise2's particular forte is the comparison of DNA sequence at the level
  of its protein translation. This comparison allows the simultaneous
  prediction of say gene structure with homology based alignment.
  .
  Wise2 also contains other algorithms, such as the venerable Smith-Waterman
  algorithm, or more modern ones such as Stephen Altschul's generalised
  gap penalties, or even experimental ones developed in house, such as
  dba. The development of these algorithms is due to the ease of developing
  such algorithms in the environment used by Wise2.
  .
  Wise2 has also been written with an eye for reuse and maintainability.
  Although it is a pure C package you can access its functionality
  directly in Perl. Parts of the package (or the entire package) can
  be used by other C or C++ programs without namespace clashes as all
  externally linked variables have the unique identifier Wise2 prepended.

drwxr-xr-x root/root         0 2020-04-18 15:57 ./
drwxr-xr-x root/root         0 2020-04-18 15:57 ./usr/
drwxr-xr-x root/root         0 2020-04-18 15:57 ./usr/bin/
-rwxr-xr-x root/root    325888 2020-04-18 15:57 ./usr/bin/dba
-rwxr-xr-x root/root    219320 2020-04-18 15:57 ./usr/bin/dnal
-rwxr-xr-x root/root   1872248 2020-04-18 15:57 ./usr/bin/estwise
-rwxr-xr-x root/root   1880536 2020-04-18 15:57 ./usr/bin/estwisedb
-rwxr-xr-x root/root   1880536 2020-04-18 15:57 ./usr/bin/genewise
-rwxr-xr-x root/root   1884728 2020-04-18 15:57 ./usr/bin/genewisedb
-rwxr-xr-x root/root    362680 2020-04-18 15:57 ./usr/bin/genomewise
-rwxr-xr-x root/root    391352 2020-04-18 15:57 ./usr/bin/promoterwise
-rwxr-xr-x root/root    325816 2020-04-18 15:57 ./usr/bin/psw
-rwxr-xr-x root/root    329992 2020-04-18 15:57 ./usr/bin/pswdb
-rwxr-xr-x root/root    469176 2020-04-18 15:57 ./usr/bin/scanwise
-rwxr-xr-x root/root    194736 2020-04-18 15:57 ./usr/bin/scanwise_server
drwxr-xr-x root/root         0 2020-04-18 15:57 ./usr/share/
drwxr-xr-x root/root         0 2020-04-18 15:57 ./usr/share/doc/
drwxr-xr-x root/root         0 2020-04-18 15:57 ./usr/share/doc/wise/
-rw-r--r-- root/root      1973 2007-07-01 20:46 ./usr/share/doc/wise/README
-rw-r--r-- root/root       320 2020-04-18 15:57 ./usr/share/doc/wise/README.Debian
-rw-r--r-- root/root      3433 2020-04-18 15:57 ./usr/share/doc/wise/changelog.Debian.gz
-rw-r--r-- root/root      4297 2020-04-18 15:57 ./usr/share/doc/wise/copyright
-rw-r--r-- root/root       312 2020-04-18 15:57 ./usr/share/doc/wise/run-unit-test
drwxr-xr-x root/root         0 2020-04-18 15:57 ./usr/share/man/
drwxr-xr-x root/root         0 2020-04-18 15:57 ./usr/share/man/man1/
-rw-r--r-- root/root       846 2020-04-18 15:57 ./usr/share/man/man1/dba.1.gz
-rw-r--r-- root/root       557 2020-04-18 15:57 ./usr/share/man/man1/dnal.1.gz
-rw-r--r-- root/root       595 2020-04-18 15:57 ./usr/share/man/man1/estwise.1.gz
-rw-r--r-- root/root       594 2020-04-18 15:57 ./usr/share/man/man1/estwisedb.1.gz
-rw-r--r-- root/root       594 2020-04-18 15:57 ./usr/share/man/man1/genewise.1.gz
-rw-r--r-- root/root       595 2020-04-18 15:57 ./usr/share/man/man1/genewisedb.1.gz
-rw-r--r-- root/root       605 2020-04-18 15:57 ./usr/share/man/man1/genomewise.1.gz
-rw-r--r-- root/root       592 2020-04-18 15:57 ./usr/share/man/man1/promoterwise.1.gz
-rw-r--r-- root/root       685 2020-04-18 15:57 ./usr/share/man/man1/psw.1.gz
-rw-r--r-- root/root       585 2020-04-18 15:57 ./usr/share/man/man1/pswdb.1.gz
-rw-r--r-- root/root       601 2020-04-18 15:57 ./usr/share/man/man1/scanwise.1.gz
-rw-r--r-- root/root       584 2020-04-18 15:57 ./usr/share/man/man1/scanwise_server.1.gz


lintian
-------


Setup apt archive
-----------------

Merged Build-Depends: lintian:arm64
Filtered Build-Depends: lintian:arm64
dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-lintian-dummy.deb'.
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Installing build dependencies
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Reading state information...
The following additional packages will be installed:
  diffstat gpg gpgconf libaliased-perl libapt-pkg-perl libassuan0
  libb-hooks-endofscope-perl libb-hooks-op-check-perl libcapture-tiny-perl
  libclass-data-inheritable-perl libclass-method-modifiers-perl
  libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl
  libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl
  libdata-optlist-perl libdata-validate-domain-perl libdevel-callchecker-perl
  libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl
  libemail-address-xs-perl libexception-class-perl libexporter-tiny-perl
  libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl
  libhtml-html5-entities-perl libimport-into-perl libipc-run3-perl
  libipc-system-simple-perl libiterator-perl libiterator-util-perl
  libjson-maybexs-perl liblist-compare-perl liblist-moreutils-perl
  liblist-moreutils-xs-perl liblist-utilsby-perl liblzo2-2 libmarkdown2
  libmodule-implementation-perl libmodule-runtime-perl libmoo-perl
  libmoox-aliases-perl libmouse-perl libnamespace-clean-perl
  libnet-domain-tld-perl libnumber-compare-perl libpackage-stash-perl
  libparams-classify-perl libparams-util-perl libpath-tiny-perl
  libperlio-gzip-perl libproc-processtable-perl librole-tiny-perl
  libsereal-decoder-perl libsereal-encoder-perl libstrictures-perl
  libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl
  libsub-install-perl libsub-name-perl libsub-quote-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 libtype-tiny-perl libunicode-utf8-perl
  liburi-perl libvariable-magic-perl libyaml-0-2 libyaml-libyaml-perl lintian
  lzip lzop patchutils unzip
Suggested packages:
  libxml-parser-perl libscalar-number-perl libbareword-filehandles-perl
  libindirect-perl libmultidimensional-perl libdevel-lexalias-perl libwww-perl
  binutils-multiarch libtext-template-perl zip
Recommended packages:
  gnupg libpackage-stash-xs-perl libref-util-perl libtype-tiny-xs-perl
The following NEW packages will be installed:
  diffstat gpg gpgconf libaliased-perl libapt-pkg-perl libassuan0
  libb-hooks-endofscope-perl libb-hooks-op-check-perl libcapture-tiny-perl
  libclass-data-inheritable-perl libclass-method-modifiers-perl
  libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl
  libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl
  libdata-optlist-perl libdata-validate-domain-perl libdevel-callchecker-perl
  libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl
  libemail-address-xs-perl libexception-class-perl libexporter-tiny-perl
  libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl
  libhtml-html5-entities-perl libimport-into-perl libipc-run3-perl
  libipc-system-simple-perl libiterator-perl libiterator-util-perl
  libjson-maybexs-perl liblist-compare-perl liblist-moreutils-perl
  liblist-moreutils-xs-perl liblist-utilsby-perl liblzo2-2 libmarkdown2
  libmodule-implementation-perl libmodule-runtime-perl libmoo-perl
  libmoox-aliases-perl libmouse-perl libnamespace-clean-perl
  libnet-domain-tld-perl libnumber-compare-perl libpackage-stash-perl
  libparams-classify-perl libparams-util-perl libpath-tiny-perl
  libperlio-gzip-perl libproc-processtable-perl librole-tiny-perl
  libsereal-decoder-perl libsereal-encoder-perl libstrictures-perl
  libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl
  libsub-install-perl libsub-name-perl libsub-quote-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 libtype-tiny-perl libunicode-utf8-perl
  liburi-perl libvariable-magic-perl libyaml-0-2 libyaml-libyaml-perl lintian
  lzip lzop patchutils sbuild-build-depends-lintian-dummy:amd64 unzip
0 upgraded, 86 newly installed, 0 to remove and 0 not upgraded.
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Setting up libapt-pkg-perl (0.1.40) ...
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Setting up libdynaloader-functions-perl (0.003-1.1) ...
Setting up libtext-glob-perl (0.11-1) ...
Setting up libclass-method-modifiers-perl (2.13-1) ...
Setting up liblist-compare-perl (0.55-1) ...
Setting up libclone-perl (0.45-1+b1) ...
Setting up libyaml-0-2:arm64 (0.2.2-1) ...
Setting up libsub-identify-perl (0.14-1+b3) ...
Setting up libcpanel-json-xs-perl (4.25-1+b1) ...
Setting up libdevel-size-perl (0.83-1+b2) ...
Setting up unzip (6.0-26) ...
Setting up libyaml-libyaml-perl (0.82+repack-1+b1) ...
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Setting up liblzo2-2:arm64 (2.10-2) ...
Setting up libtime-moment-perl (0.44-1+b3) ...
Setting up libassuan0:arm64 (2.5.4-1) ...
Setting up libconfig-tiny-perl (2.26-1) ...
Setting up libsereal-encoder-perl (4.018+ds-1+b1) ...
Setting up liblist-utilsby-perl (0.11-1) ...
Setting up libsub-install-perl (0.928-1.1) ...
Setting up libnumber-compare-perl (0.03-1.1) ...
Setting up patchutils (0.4.2-1) ...
Setting up libjson-maybexs-perl (1.004003-1) ...
Setting up libclass-data-inheritable-perl (0.08-3) ...
Setting up libfile-find-rule-perl (0.34-1) ...
Setting up libipc-system-simple-perl (1.30-1) ...
Setting up libnet-domain-tld-perl (1.75-1.1) ...
Setting up lzip (1.22-3) ...
Setting up diffstat (1.64-1) ...
Setting up libvariable-magic-perl (0.62-1+b3) ...
Setting up libb-hooks-op-check-perl (0.22-1+b3) ...
Setting up liblist-moreutils-xs-perl (0.430-2) ...
Setting up libparams-util-perl (1.102-1+b1) ...
Setting up libtime-duration-perl (1.21-1) ...
Setting up libtext-xslate-perl (3.5.8-1+b1) ...
Setting up libsub-exporter-progressive-perl (0.001013-1) ...
Setting up libcapture-tiny-perl (0.48-1) ...
Setting up libtimedate-perl (2.3300-2) ...
Setting up libsub-name-perl (0.26-1+b1) ...
Setting up libdata-validate-domain-perl (0.10-1.1) ...
Setting up libproc-processtable-perl (0.59-2+b1) ...
Setting up libpath-tiny-perl (0.118-1) ...
Setting up lzop (1.04-2) ...
Setting up gpgconf (2.2.27-2) ...
Setting up librole-tiny-perl (2.002004-1) ...
Setting up libipc-run3-perl (0.048-2) ...
Setting up libaliased-perl (0.34-1.1) ...
Setting up libstrictures-perl (2.000006-1) ...
Setting up libsub-quote-perl (2.006006-1) ...
Setting up libdevel-stacktrace-perl (2.0400-1) ...
Setting up libclass-xsaccessor-perl (1.19-3+b7) ...
Setting up libexporter-tiny-perl (1.002002-1) ...
Setting up libfont-ttf-perl (1.06-1.1) ...
Setting up libtext-levenshteinxs-perl (0.03-4+b8) ...
Setting up libperlio-gzip-perl (0.19-1+b7) ...
Setting up libhtml-html5-entities-perl (0.004-1.1) ...
Setting up libsereal-decoder-perl (4.018+ds-1+b1) ...
Setting up libmarkdown2:arm64 (2.2.6-1) ...
Setting up liburi-perl (5.08-1) ...
Setting up gpg (2.2.27-2) ...
Setting up libemail-address-xs-perl (1.04-1+b3) ...
Setting up libfile-basedir-perl (0.08-1) ...
Setting up liblist-moreutils-perl (0.430-2) ...
Setting up libtype-tiny-perl (1.012002-1) ...
Setting up libtext-markdown-discount-perl:arm64 (0.12-1+b1) ...
Setting up libexception-class-perl (1.44-1) ...
Setting up libdevel-callchecker-perl (0.008-1+b2) ...
Setting up libdata-optlist-perl (0.110-1.1) ...
Setting up libsub-exporter-perl (0.987-1) ...
Setting up libiterator-perl (0.03+ds1-1.1) ...
Setting up libiterator-util-perl (0.02+ds1-1.1) ...
Setting up libparams-classify-perl (0.015-1+b3) ...
Setting up libmodule-runtime-perl (0.016-1) ...
Setting up libdata-dpath-perl (0.58-1) ...
Setting up libmodule-implementation-perl (0.09-1.1) ...
Setting up libpackage-stash-perl (0.39-1) ...
Setting up libimport-into-perl (1.002005-1) ...
Setting up libmoo-perl (2.004004-1) ...
Setting up libmoox-aliases-perl (0.001006-1.1) ...
Setting up libb-hooks-endofscope-perl (0.24-1.1) ...
Setting up libnamespace-clean-perl (0.27-1) ...
Setting up lintian (2.104.0) ...
Setting up sbuild-build-depends-lintian-dummy:amd64 (0.invalid.0) ...
Processing triggers for man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Processing triggers for libc-bin (2.31-13) ...

I: Lintian run was successful.

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| Post Build                                                                   |
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| Cleanup                                                                      |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use

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| Summary                                                                      |
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Build Architecture: arm64
Build Profiles: cross nocheck
Build Type: any
Build-Space: 188940
Build-Time: 437
Distribution: unstable
Foreign Architectures: amd64
Host Architecture: amd64
Install-Time: 148
Job: wise_2.4.1-23
Lintian: pass
Machine Architecture: arm64
Package: wise
Package-Time: 610
Source-Version: 2.4.1-23
Space: 188940
Status: successful
Version: 2.4.1-23
--------------------------------------------------------------------------------
Finished at 2021-07-17T08:20:38Z
Build needed 00:10:10, 188940k disk space