sbuild (Debian sbuild) 0.78.1 (09 February 2019) on gcc131.bak.milne.osuosl.org

+==============================================================================+
| wise 2.4.1-23 (arm64)                        Thu, 24 Sep 2020 15:57:43 +0000 |
+==============================================================================+

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

I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-5777e886-b1bb-4245-b2a2-d6af2869b23a' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/wise-rMm58v/resolver-1PklrS' with '<<RESOLVERDIR>>'

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| Update chroot                                                                |
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Get:1 http://debian.oregonstate.edu/debian unstable InRelease [146 kB]
Get:2 http://debian.oregonstate.edu/debian unstable/main Sources.diff/Index [27.9 kB]
Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 Packages.diff/Index [27.9 kB]
Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2020-09-24-0810.01.pdiff [3570 B]
Get:5 http://debian.oregonstate.edu/debian unstable/main Sources 2020-09-24-1413.21.pdiff [27.4 kB]
Get:5 http://debian.oregonstate.edu/debian unstable/main Sources 2020-09-24-1413.21.pdiff [27.4 kB]
Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-09-24-0810.01.pdiff [2225 B]
Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-09-24-1413.21.pdiff [29.4 kB]
Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-09-24-1413.21.pdiff [29.4 kB]
Get:8 http://debian.oregonstate.edu/debian unstable/main arm64 Packages [8247 kB]
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The following packages will be upgraded:
  bsdutils coreutils fdisk libblkid1 libfdisk1 libmount1 libsmartcols1
  libuuid1 mount util-linux
10 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 5411 kB of archives.
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Get:1 http://debian.oregonstate.edu/debian unstable/main amd64 bsdutils amd64 1:2.36-3+b1 [148 kB]
Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 coreutils amd64 8.32-4+b1 [2867 kB]
Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libblkid1 amd64 2.36-3+b1 [195 kB]
Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libuuid1 amd64 2.36-3+b1 [82.7 kB]
Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libfdisk1 amd64 2.36-3+b1 [238 kB]
Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libmount1 amd64 2.36-3+b1 [212 kB]
Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 libsmartcols1 amd64 2.36-3+b1 [158 kB]
Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 fdisk amd64 2.36-3+b1 [190 kB]
Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 util-linux amd64 2.36-3+b1 [1136 kB]
Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 mount amd64 2.36-3+b1 [184 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Processing triggers for libc-bin (2.31-3) ...

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| Fetch source files                                                           |
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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://debian.oregonstate.edu/debian unstable/main wise 2.4.1-23 (dsc) [2179 B]
Get:2 http://debian.oregonstate.edu/debian unstable/main wise 2.4.1-23 (tar) [3410 kB]
Get:3 http://debian.oregonstate.edu/debian unstable/main wise 2.4.1-23 (diff) [27.2 kB]
Fetched 3440 kB in 0s (33.9 MB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/wise-rMm58v/wise-2.4.1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/wise-rMm58v' 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:amd64, fakeroot:amd64, crossbuild-essential-arm64:amd64, libc-dev:arm64, libstdc++-dev:arm64
Filtered Build-Depends: debhelper-compat (= 12), texlive-latex-base, texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-arm64:amd64, libc-dev:arm64, libstdc++-dev:arm64
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<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 [534 B]
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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-aarch64-linux-gnu
  bsdextrautils build-essential cpp-10-aarch64-linux-gnu cpp-aarch64-linux-gnu
  cross-config crossbuild-essential-arm64 debhelper dh-autoreconf
  dh-strip-nondeterminism docbook docbook-to-man dpkg-cross dpkg-dev dwz file
  fontconfig-config fonts-dejavu-core fonts-lmodern fonts-urw-base35 g++
  g++-10 g++-10-aarch64-linux-gnu g++-aarch64-linux-gnu
  gcc-10-aarch64-linux-gnu gcc-10-aarch64-linux-gnu-base gcc-10-base:arm64
  gcc-10-cross-base gcc-9-base:arm64 gcc-aarch64-linux-gnu gettext
  gettext-base ghostscript groff-base hevea intltool-debian
  libarchive-zip-perl libasan5:arm64 libasan6-arm64-cross libatomic1:arm64
  libatomic1-arm64-cross libavahi-client3 libavahi-common-data
  libavahi-common3 libblkid-dev:arm64 libblkid1:arm64 libbrotli1 libbsd0
  libc6:arm64 libc6-arm64-cross libc6-dev libc6-dev:arm64
  libc6-dev-arm64-cross libcairo2 libconfig-auto-perl libconfig-inifiles-perl
  libcroco3 libcrypt-dev libcrypt-dev:arm64 libcrypt1:arm64 libcups2
  libdatrie1 libdbus-1-3 libdebhelper-perl libdebian-dpkgcross-perl
  libdpkg-perl libelf1 libexpat1 libffi-dev:arm64 libffi7:arm64
  libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl
  libfontconfig1 libfontenc1 libfreetype6 libgcc-10-dev-arm64-cross
  libgcc-9-dev:arm64 libgcc-s1:arm64 libgcc-s1-arm64-cross libglib2.0-0
  libglib2.0-0:arm64 libglib2.0-bin libglib2.0-data libglib2.0-dev:arm64
  libglib2.0-dev-bin libgomp1:arm64 libgomp1-arm64-cross libgraphite2-3 libgs9
  libgs9-common libgssapi-krb5-2 libharfbuzz0b libice6 libicu67 libidn11
  libijs-0.35 libio-string-perl libitm1:arm64 libitm1-arm64-cross libjbig0
  libjbig2dec0 libjpeg62-turbo libjs-jquery libk5crypto3 libkeyutils1
  libkpathsea6 libkrb5-3 libkrb5support0 liblcms2-2 liblocale-gettext-perl
  liblsan0:arm64 liblsan0-arm64-cross libmagic-mgc libmagic1
  libmime-charset-perl libmount-dev:arm64 libmount1:arm64 libnetpbm10
  libopenjp2-7 libosp5 libpaper-utils libpaper1 libpcre16-3:arm64
  libpcre2-16-0:arm64 libpcre2-32-0:arm64 libpcre2-8-0:arm64
  libpcre2-dev:arm64 libpcre2-posix2:arm64 libpcre3:arm64 libpcre3-dev:arm64
  libpcre32-3:arm64 libpcrecpp0v5:arm64 libperl5.30 libpipeline1 libpixman-1-0
  libpng16-16 libptexenc1 libpython3-stdlib libpython3.8-minimal
  libpython3.8-stdlib libreadline8 libselinux1:arm64 libselinux1-dev:arm64
  libsepol1:arm64 libsepol1-dev:arm64 libsigsegv2 libsm6 libsombok3
  libsqlite3-0 libssl1.1 libstdc++-10-dev libstdc++-10-dev-arm64-cross
  libstdc++-9-dev:arm64 libstdc++6:arm64 libstdc++6-arm64-cross
  libsub-override-perl libsynctex2 libteckit0 libtexlua53 libtexluajit2
  libthai-data libthai0 libtiff5 libtool libtsan0:arm64 libtsan0-arm64-cross
  libubsan1:arm64 libubsan1-arm64-cross libuchardet0 libunicode-linebreak-perl
  libuuid1:arm64 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:arm64 linux-libc-dev-arm64-cross lmodern m4
  man-db mime-support netpbm node-jquery opensp perl perl-modules-5.30
  pkg-config po-debconf poppler-data python3 python3-distutils python3-lib2to3
  python3-minimal python3.8 python3.8-minimal readline-common sensible-utils
  sgml-base sgml-data t1utils tex-common texlive-base texlive-binaries
  texlive-extra-utils texlive-latex-base texlive-luatex texlive-plain-generic
  ucf uuid-dev:arm64 x11-common xdg-utils xfonts-encodings xfonts-utils
  xml-core zlib1g:arm64 zlib1g-dev:arm64
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-10-locales
  cpp-doc dh-make docbook-defguide docbook-dsssl docbook-xml psgml
  binutils-multiarch debian-keyring fonts-freefont-otf | fonts-freefont-ttf
  fonts-texgyre g++-multilib g++-10-multilib gcc-10-doc manpages-dev flex
  bison gdb-aarch64-linux-gnu gcc-doc gettext-doc libasprintf-dev
  libgettextpo-dev ghostscript-x groff hevea-doc texlive-latex-extra
  glibc-doc:arm64 libc-l10n:arm64 locales:arm64 glibc-doc manpages-dev:arm64
  cups-common gnupg git bzr libgirepository1.0-dev:arm64 libglib2.0-doc:arm64
  libgdk-pixbuf2.0-bin | libgdk-pixbuf2.0-dev libxml2-utils krb5-doc krb5-user
  liblcms2-utils libencode-hanextra-perl libpod2-base-perl libstdc++-10-doc
  libstdc++-9-doc:arm64 libtool-doc gfortran | fortran95-compiler gcj-jdk
  libyaml-shell-perl m4-doc apparmor less www-browser doc-base perl-doc
  libterm-readline-gnu-perl | libterm-readline-perl-perl
  libtap-harness-archive-perl 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 python3.8-venv python3.8-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:
  gnupg libalgorithm-merge-perl curl | wget | lynx libidn2-0:arm64 dbus
  libfile-fcntllock-perl libarchive-cpio-perl shared-mime-info xdg-user-dirs
  shared-mime-info:arm64 xdg-user-dirs:arm64 fonts-droid-fallback
  javascript-common krb5-locales libltdl-dev uuid-runtime:arm64 libwww-perl
  libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl netbase
  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-aarch64-linux-gnu
  bsdextrautils build-essential cpp-10-aarch64-linux-gnu cpp-aarch64-linux-gnu
  cross-config crossbuild-essential-arm64 debhelper dh-autoreconf
  dh-strip-nondeterminism docbook docbook-to-man dpkg-cross dpkg-dev dwz file
  fontconfig-config fonts-dejavu-core fonts-lmodern fonts-urw-base35 g++
  g++-10 g++-10-aarch64-linux-gnu g++-aarch64-linux-gnu
  gcc-10-aarch64-linux-gnu gcc-10-aarch64-linux-gnu-base gcc-10-base:arm64
  gcc-10-cross-base gcc-9-base:arm64 gcc-aarch64-linux-gnu gettext
  gettext-base ghostscript groff-base hevea intltool-debian
  libarchive-zip-perl libasan5:arm64 libasan6-arm64-cross libatomic1:arm64
  libatomic1-arm64-cross libavahi-client3 libavahi-common-data
  libavahi-common3 libblkid-dev:arm64 libblkid1:arm64 libbrotli1 libbsd0
  libc6:arm64 libc6-arm64-cross libc6-dev libc6-dev:arm64
  libc6-dev-arm64-cross libcairo2 libconfig-auto-perl libconfig-inifiles-perl
  libcroco3 libcrypt-dev libcrypt-dev:arm64 libcrypt1:arm64 libcups2
  libdatrie1 libdbus-1-3 libdebhelper-perl libdebian-dpkgcross-perl
  libdpkg-perl libelf1 libexpat1 libffi-dev:arm64 libffi7:arm64
  libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl
  libfontconfig1 libfontenc1 libfreetype6 libgcc-10-dev-arm64-cross
  libgcc-9-dev:arm64 libgcc-s1:arm64 libgcc-s1-arm64-cross libglib2.0-0
  libglib2.0-0:arm64 libglib2.0-bin libglib2.0-data libglib2.0-dev:arm64
  libglib2.0-dev-bin libgomp1:arm64 libgomp1-arm64-cross libgraphite2-3 libgs9
  libgs9-common libgssapi-krb5-2 libharfbuzz0b libice6 libicu67 libidn11
  libijs-0.35 libio-string-perl libitm1:arm64 libitm1-arm64-cross libjbig0
  libjbig2dec0 libjpeg62-turbo libjs-jquery libk5crypto3 libkeyutils1
  libkpathsea6 libkrb5-3 libkrb5support0 liblcms2-2 liblocale-gettext-perl
  liblsan0:arm64 liblsan0-arm64-cross libmagic-mgc libmagic1
  libmime-charset-perl libmount-dev:arm64 libmount1:arm64 libnetpbm10
  libopenjp2-7 libosp5 libpaper-utils libpaper1 libpcre16-3:arm64
  libpcre2-16-0:arm64 libpcre2-32-0:arm64 libpcre2-8-0:arm64
  libpcre2-dev:arm64 libpcre2-posix2:arm64 libpcre3:arm64 libpcre3-dev:arm64
  libpcre32-3:arm64 libpcrecpp0v5:arm64 libperl5.30 libpipeline1 libpixman-1-0
  libpng16-16 libptexenc1 libpython3-stdlib libpython3.8-minimal
  libpython3.8-stdlib libreadline8 libselinux1:arm64 libselinux1-dev:arm64
  libsepol1:arm64 libsepol1-dev:arm64 libsigsegv2 libsm6 libsombok3
  libsqlite3-0 libssl1.1 libstdc++-10-dev libstdc++-10-dev-arm64-cross
  libstdc++-9-dev:arm64 libstdc++6:arm64 libstdc++6-arm64-cross
  libsub-override-perl libsynctex2 libteckit0 libtexlua53 libtexluajit2
  libthai-data libthai0 libtiff5 libtool libtsan0:arm64 libtsan0-arm64-cross
  libubsan1:arm64 libubsan1-arm64-cross libuchardet0 libunicode-linebreak-perl
  libuuid1:arm64 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:arm64 linux-libc-dev-arm64-cross lmodern m4
  man-db mime-support netpbm node-jquery opensp perl perl-modules-5.30
  pkg-config po-debconf poppler-data python3 python3-distutils python3-lib2to3
  python3-minimal python3.8 python3.8-minimal readline-common
  sbuild-build-depends-main-dummy:arm64 sensible-utils sgml-base sgml-data
  t1utils tex-common texlive-base texlive-binaries texlive-extra-utils
  texlive-latex-base texlive-luatex texlive-plain-generic ucf uuid-dev:arm64
  x11-common xdg-utils xfonts-encodings xfonts-utils xml-core zlib1g:arm64
  zlib1g-dev:arm64
0 upgraded, 241 newly installed, 0 to remove and 0 not upgraded.
Need to get 285 MB of archives.
After this operation, 926 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://debian.oregonstate.edu/debian unstable/main amd64 bsdextrautils amd64 2.36-3+b1 [140 kB]
Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB]
Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-5 [920 kB]
Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB]
Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.9.3-2 [1314 kB]
Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 perl-modules-5.30 all 5.30.3-4 [2806 kB]
Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libperl5.30 amd64 5.30.3-4 [4019 kB]
Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 perl amd64 5.30.3-4 [290 kB]
Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-4 [18.8 kB]
Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 poppler-data all 0.4.9-2 [1473 kB]
Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libssl1.1 amd64 1.1.1g-1 [1543 kB]
Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 libpython3.8-minimal amd64 3.8.6~rc1-2 [760 kB]
Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libexpat1 amd64 2.2.9-1 [94.3 kB]
Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 python3.8-minimal amd64 3.8.6~rc1-2 [1865 kB]
Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 python3-minimal amd64 3.8.2-3 [37.6 kB]
Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 mime-support all 3.64 [37.8 kB]
Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 readline-common all 8.0-4 [72.5 kB]
Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libreadline8 amd64 8.0-4 [160 kB]
Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 libsqlite3-0 amd64 3.33.0-1 [790 kB]
Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libpython3.8-stdlib amd64 3.8.6~rc1-2 [1722 kB]
Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 python3.8 amd64 3.8.6~rc1-2 [422 kB]
Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 libpython3-stdlib amd64 3.8.2-3 [20.8 kB]
Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 python3 amd64 3.8.2-3 [63.7 kB]
Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 sgml-base all 1.30 [15.1 kB]
Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0043 [74.0 kB]
Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 tex-common all 6.15 [53.5 kB]
Get:29 http://debian.oregonstate.edu/debian unstable/main arm64 gcc-10-base arm64 10.2.0-9 [199 kB]
Get:30 http://debian.oregonstate.edu/debian unstable/main arm64 gcc-9-base arm64 9.3.0-18 [197 kB]
Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.38-5 [262 kB]
Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.38-5 [120 kB]
Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.38-5 [67.9 kB]
Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-10 [123 kB]
Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB]
Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-4 [203 kB]
Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11.1 [341 kB]
Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB]
Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.2-4 [801 kB]
Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-10 [435 kB]
Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-aarch64-linux-gnu amd64 2.35.1-1 [2804 kB]
Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libcrypt-dev amd64 1:4.4.17-1 [104 kB]
Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev amd64 2.31-3 [2395 kB]
Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-10-dev amd64 10.2.0-9 [1737 kB]
Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 g++-10 amd64 10.2.0-9 [8664 kB]
Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 g++ amd64 4:10.2.0-1 [1644 B]
Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 libdpkg-perl all 1.20.5 [1473 kB]
Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-dev all 1.20.5 [1909 kB]
Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 build-essential amd64 12.8 [7640 B]
Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-10-aarch64-linux-gnu-base amd64 10.2.0-9cross1 [199 kB]
Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-10-aarch64-linux-gnu amd64 10.2.0-9cross1 [7820 kB]
Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-aarch64-linux-gnu amd64 4:10.2.0-1 [16.8 kB]
Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-3.1 [39.9 kB]
Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-10-cross-base all 10.2.0-9cross1 [195 kB]
Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-arm64-cross all 2.31-1cross2 [1260 kB]
Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-s1-arm64-cross all 10.2.0-9cross1 [34.5 kB]
Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-arm64-cross all 10.2.0-9cross1 [89.6 kB]
Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libitm1-arm64-cross all 10.2.0-9cross1 [23.3 kB]
Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-arm64-cross all 10.2.0-9cross1 [9240 B]
Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 libasan6-arm64-cross all 10.2.0-9cross1 [298 kB]
Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 liblsan0-arm64-cross all 10.2.0-9cross1 [125 kB]
Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libtsan0-arm64-cross all 10.2.0-9cross1 [285 kB]
Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-arm64-cross all 10.2.0-9cross1 [411 kB]
Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-arm64-cross all 10.2.0-9cross1 [122 kB]
Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-10-dev-arm64-cross all 10.2.0-9cross1 [880 kB]
Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-10-aarch64-linux-gnu amd64 10.2.0-9cross1 [15.6 MB]
Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-aarch64-linux-gnu amd64 4:10.2.0-1 [1456 B]
Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-arm64-cross all 5.7.6-1cross2 [1208 kB]
Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-arm64-cross all 2.31-1cross2 [2067 kB]
Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-10-dev-arm64-cross all 10.2.0-9cross1 [1678 kB]
Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 g++-10-aarch64-linux-gnu amd64 10.2.0-9cross1 [8478 kB]
Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 g++-aarch64-linux-gnu amd64 4:10.2.0-1 [1176 B]
Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000003-1 [52.1 kB]
Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB]
Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 libicu67 amd64 67.1-4 [8624 kB]
Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.10+dfsg-6 [692 kB]
Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB]
Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB]
Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB]
Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-2 [343 kB]
Get:81 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB]
Get:82 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.30-1 [67.7 kB]
Get:83 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB]
Get:84 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB]
Get:85 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB]
Get:86 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-3.1 [38.9 kB]
Get:87 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-3.1 [49.9 kB]
Get:88 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-arm64 all 12.8 [6644 B]
Get:89 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-14 [513 kB]
Get:90 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB]
Get:91 http://debian.oregonstate.edu/debian unstable/main amd64 libdebhelper-perl all 13.2.1 [188 kB]
Get:92 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get:93 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB]
Get:94 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:95 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:96 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.181-1 [164 kB]
Get:97 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.13-5 [151 kB]
Get:98 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.66.0-2 [1361 kB]
Get:99 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.13-1 [146 kB]
Get:100 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-10 [1303 kB]
Get:101 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:102 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB]
Get:103 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 13.2.1 [1007 kB]
Get:104 http://debian.oregonstate.edu/debian unstable/main amd64 xml-core all 0.18+nmu1 [23.8 kB]
Get:105 http://debian.oregonstate.edu/debian unstable/main amd64 sgml-data all 2.0.11 [179 kB]
Get:106 http://debian.oregonstate.edu/debian unstable/main amd64 docbook all 4.5-6 [129 kB]
Get:107 http://debian.oregonstate.edu/debian unstable/main amd64 libosp5 amd64 1.5.2-13+b1 [948 kB]
Get:108 http://debian.oregonstate.edu/debian unstable/main amd64 opensp amd64 1.5.2-13+b1 [449 kB]
Get:109 http://debian.oregonstate.edu/debian unstable/main amd64 docbook-to-man amd64 1:2.0.0-45 [77.4 kB]
Get:110 http://debian.oregonstate.edu/debian unstable/main amd64 fonts-dejavu-core all 2.37-2 [1069 kB]
Get:111 http://debian.oregonstate.edu/debian unstable/main amd64 fonts-urw-base35 all 20200910-1 [6367 kB]
Get:112 http://debian.oregonstate.edu/debian unstable/main amd64 fontconfig-config all 2.13.1-4.2 [281 kB]
Get:113 http://debian.oregonstate.edu/debian unstable/main amd64 fonts-lmodern all 2.004.5-6 [4539 kB]
Get:114 http://debian.oregonstate.edu/debian unstable/main amd64 libgs9-common all 9.53.1~dfsg-2 [732 kB]
Get:115 http://debian.oregonstate.edu/debian unstable/main amd64 libavahi-common-data amd64 0.8-3 [126 kB]
Get:116 http://debian.oregonstate.edu/debian unstable/main amd64 libavahi-common3 amd64 0.8-3 [58.3 kB]
Get:117 http://debian.oregonstate.edu/debian unstable/main amd64 libdbus-1-3 amd64 1.12.20-1 [217 kB]
Get:118 http://debian.oregonstate.edu/debian unstable/main amd64 libavahi-client3 amd64 0.8-3 [61.7 kB]
Get:119 http://debian.oregonstate.edu/debian unstable/main amd64 libkrb5support0 amd64 1.17-10 [64.6 kB]
Get:120 http://debian.oregonstate.edu/debian unstable/main amd64 libk5crypto3 amd64 1.17-10 [115 kB]
Get:121 http://debian.oregonstate.edu/debian unstable/main amd64 libkeyutils1 amd64 1.6.1-2 [15.4 kB]
Get:122 http://debian.oregonstate.edu/debian unstable/main amd64 libkrb5-3 amd64 1.17-10 [366 kB]
Get:123 http://debian.oregonstate.edu/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.17-10 [156 kB]
Get:124 http://debian.oregonstate.edu/debian unstable/main amd64 libcups2 amd64 2.3.3-3 [348 kB]
Get:125 http://debian.oregonstate.edu/debian unstable/main amd64 libbrotli1 amd64 1.0.9-2 [287 kB]
Get:126 http://debian.oregonstate.edu/debian unstable/main amd64 libpng16-16 amd64 1.6.37-3 [294 kB]
Get:127 http://debian.oregonstate.edu/debian unstable/main amd64 libfreetype6 amd64 2.10.2+dfsg-3 [409 kB]
Get:128 http://debian.oregonstate.edu/debian unstable/main amd64 libfontconfig1 amd64 2.13.1-4.2 [347 kB]
Get:129 http://debian.oregonstate.edu/debian unstable/main amd64 libidn11 amd64 1.33-2.4 [116 kB]
Get:130 http://debian.oregonstate.edu/debian unstable/main amd64 libijs-0.35 amd64 0.35-15 [16.4 kB]
Get:131 http://debian.oregonstate.edu/debian unstable/main amd64 libjbig2dec0 amd64 0.19-1 [66.9 kB]
Get:132 http://debian.oregonstate.edu/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.0.5-1.1 [149 kB]
Get:133 http://debian.oregonstate.edu/debian unstable/main amd64 liblcms2-2 amd64 2.9-4+b1 [146 kB]
Get:134 http://debian.oregonstate.edu/debian unstable/main amd64 libopenjp2-7 amd64 2.3.1-1 [159 kB]
Get:135 http://debian.oregonstate.edu/debian unstable/main amd64 libpaper1 amd64 1.1.28+b1 [21.6 kB]
Get:136 http://debian.oregonstate.edu/debian unstable/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB]
Get:137 http://debian.oregonstate.edu/debian unstable/main amd64 libwebp6 amd64 0.6.1-2+b1 [261 kB]
Get:138 http://debian.oregonstate.edu/debian unstable/main amd64 libtiff5 amd64 4.1.0+git191117-2 [271 kB]
Get:139 http://debian.oregonstate.edu/debian unstable/main amd64 libgs9 amd64 9.53.1~dfsg-2 [2224 kB]
Get:140 http://debian.oregonstate.edu/debian unstable/main amd64 ghostscript amd64 9.53.1~dfsg-2 [96.1 kB]
Get:141 http://debian.oregonstate.edu/debian unstable/main amd64 libnetpbm10 amd64 2:10.0-15.3+b2 [86.7 kB]
Get:142 http://debian.oregonstate.edu/debian unstable/main amd64 netpbm amd64 2:10.0-15.3+b2 [1029 kB]
Get:143 http://debian.oregonstate.edu/debian unstable/main amd64 libpaper-utils amd64 1.1.28+b1 [18.3 kB]
Get:144 http://debian.oregonstate.edu/debian unstable/main amd64 libkpathsea6 amd64 2020.20200327.54578-5 [172 kB]
Get:145 http://debian.oregonstate.edu/debian unstable/main amd64 libptexenc1 amd64 2020.20200327.54578-5 [64.4 kB]
Get:146 http://debian.oregonstate.edu/debian unstable/main amd64 libsynctex2 amd64 2020.20200327.54578-5 [83.1 kB]
Get:147 http://debian.oregonstate.edu/debian unstable/main amd64 libtexlua53 amd64 2020.20200327.54578-5 [131 kB]
Get:148 http://debian.oregonstate.edu/debian unstable/main amd64 libtexluajit2 amd64 2020.20200327.54578-5 [267 kB]
Get:149 http://debian.oregonstate.edu/debian unstable/main amd64 t1utils amd64 1.41-4 [62.1 kB]
Get:150 http://debian.oregonstate.edu/debian unstable/main amd64 libpixman-1-0 amd64 0.36.0-1 [537 kB]
Get:151 http://debian.oregonstate.edu/debian unstable/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB]
Get:152 http://debian.oregonstate.edu/debian unstable/main amd64 libbsd0 amd64 0.10.0-1 [107 kB]
Get:153 http://debian.oregonstate.edu/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB]
Get:154 http://debian.oregonstate.edu/debian unstable/main amd64 libxcb1 amd64 1.14-2 [139 kB]
Get:155 http://debian.oregonstate.edu/debian unstable/main amd64 libx11-data all 2:1.6.12-1 [311 kB]
Get:156 http://debian.oregonstate.edu/debian unstable/main amd64 libx11-6 amd64 2:1.6.12-1 [770 kB]
Get:157 http://debian.oregonstate.edu/debian unstable/main amd64 libxcb-render0 amd64 1.14-2 [111 kB]
Get:158 http://debian.oregonstate.edu/debian unstable/main amd64 libxcb-shm0 amd64 1.14-2 [101 kB]
Get:159 http://debian.oregonstate.edu/debian unstable/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB]
Get:160 http://debian.oregonstate.edu/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB]
Get:161 http://debian.oregonstate.edu/debian unstable/main amd64 libcairo2 amd64 1.16.0-4 [689 kB]
Get:162 http://debian.oregonstate.edu/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB]
Get:163 http://debian.oregonstate.edu/debian unstable/main amd64 libharfbuzz0b amd64 2.6.7-1 [1467 kB]
Get:164 http://debian.oregonstate.edu/debian unstable/main amd64 libteckit0 amd64 2.5.10+ds1-3 [329 kB]
Get:165 http://debian.oregonstate.edu/debian unstable/main amd64 x11-common all 1:7.7+20 [252 kB]
Get:166 http://debian.oregonstate.edu/debian unstable/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB]
Get:167 http://debian.oregonstate.edu/debian unstable/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB]
Get:168 http://debian.oregonstate.edu/debian unstable/main amd64 libxt6 amd64 1:1.2.0-1 [189 kB]
Get:169 http://debian.oregonstate.edu/debian unstable/main amd64 libxmu6 amd64 2:1.1.2-2+b3 [60.8 kB]
Get:170 http://debian.oregonstate.edu/debian unstable/main amd64 libxpm4 amd64 1:3.5.12-1 [49.1 kB]
Get:171 http://debian.oregonstate.edu/debian unstable/main amd64 libxaw7 amd64 2:1.0.13-1+b2 [201 kB]
Get:172 http://debian.oregonstate.edu/debian unstable/main amd64 libxi6 amd64 2:1.7.10-1 [83.4 kB]
Get:173 http://debian.oregonstate.edu/debian unstable/main amd64 libzzip-0-13 amd64 0.13.62-3.2 [55.4 kB]
Get:174 http://debian.oregonstate.edu/debian unstable/main amd64 texlive-binaries amd64 2020.20200327.54578-5 [10.1 MB]
Get:175 http://debian.oregonstate.edu/debian unstable/main amd64 xdg-utils all 1.1.3-2 [74.6 kB]
Get:176 http://debian.oregonstate.edu/debian unstable/main amd64 texlive-base all 2020.20200804-3 [21.5 MB]
Get:177 http://debian.oregonstate.edu/debian unstable/main amd64 hevea amd64 2.34-2 [1863 kB]
Get:178 http://debian.oregonstate.edu/debian unstable/main arm64 libgcc-s1 arm64 10.2.0-9 [34.6 kB]
Get:179 http://debian.oregonstate.edu/debian unstable/main arm64 libcrypt1 arm64 1:4.4.17-1 [89.3 kB]
Get:180 http://debian.oregonstate.edu/debian unstable/main arm64 libc6 arm64 2.31-3 [2491 kB]
Get:181 http://debian.oregonstate.edu/debian unstable/main arm64 libasan5 arm64 9.3.0-18 [354 kB]
Get:182 http://debian.oregonstate.edu/debian unstable/main arm64 libatomic1 arm64 10.2.0-9 [9444 B]
Get:183 http://debian.oregonstate.edu/debian unstable/main arm64 libblkid1 arm64 2.36-3+b1 [188 kB]
Get:184 http://debian.oregonstate.edu/debian unstable/main arm64 linux-libc-dev arm64 5.8.10-1 [1161 kB]
Get:185 http://debian.oregonstate.edu/debian unstable/main arm64 libcrypt-dev arm64 1:4.4.17-1 [109 kB]
Get:186 http://debian.oregonstate.edu/debian unstable/main arm64 libc6-dev arm64 2.31-3 [2079 kB]
Get:187 http://debian.oregonstate.edu/debian unstable/main arm64 libuuid1 arm64 2.36-3+b1 [82.3 kB]
Get:188 http://debian.oregonstate.edu/debian unstable/main arm64 uuid-dev arm64 2.36-3+b1 [98.6 kB]
Get:189 http://debian.oregonstate.edu/debian unstable/main arm64 libblkid-dev arm64 2.36-3+b1 [231 kB]
Get:190 http://debian.oregonstate.edu/debian unstable/main amd64 libdatrie1 amd64 0.2.12-3 [39.5 kB]
Get:191 http://debian.oregonstate.edu/debian unstable/main arm64 libffi7 arm64 3.3-4 [20.5 kB]
Get:192 http://debian.oregonstate.edu/debian unstable/main arm64 libffi-dev arm64 3.3-4 [53.2 kB]
Get:193 http://debian.oregonstate.edu/debian unstable/main amd64 libfontenc1 amd64 1:1.1.4-1 [24.3 kB]
Get:194 http://debian.oregonstate.edu/debian unstable/main arm64 libgomp1 arm64 10.2.0-9 [91.6 kB]
Get:195 http://debian.oregonstate.edu/debian unstable/main arm64 libitm1 arm64 10.2.0-9 [23.8 kB]
Get:196 http://debian.oregonstate.edu/debian unstable/main arm64 liblsan0 arm64 10.2.0-9 [126 kB]
Get:197 http://debian.oregonstate.edu/debian unstable/main arm64 libtsan0 arm64 10.2.0-9 [293 kB]
Get:198 http://debian.oregonstate.edu/debian unstable/main arm64 libstdc++6 arm64 10.2.0-9 [450 kB]
Get:199 http://debian.oregonstate.edu/debian unstable/main arm64 libubsan1 arm64 10.2.0-9 [123 kB]
Get:200 http://debian.oregonstate.edu/debian unstable/main arm64 libgcc-9-dev arm64 9.3.0-18 [884 kB]
Get:201 http://debian.oregonstate.edu/debian unstable/main arm64 libpcre2-8-0 arm64 10.34-7 [208 kB]
Get:202 http://debian.oregonstate.edu/debian unstable/main arm64 libselinux1 arm64 3.1-2 [83.7 kB]
Get:203 http://debian.oregonstate.edu/debian unstable/main arm64 libmount1 arm64 2.36-3+b1 [203 kB]
Get:204 http://debian.oregonstate.edu/debian unstable/main arm64 libpcre3 arm64 2:8.39-13 [318 kB]
Get:205 http://debian.oregonstate.edu/debian unstable/main arm64 zlib1g arm64 1:1.2.11.dfsg-2 [87.9 kB]
Get:206 http://debian.oregonstate.edu/debian unstable/main arm64 libglib2.0-0 arm64 2.66.0-2 [1278 kB]
Get:207 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-data all 2.66.0-2 [1167 kB]
Get:208 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-bin amd64 2.66.0-2 [138 kB]
Get:209 http://debian.oregonstate.edu/debian unstable/main amd64 python3-lib2to3 all 3.8.5-1 [78.4 kB]
Get:210 http://debian.oregonstate.edu/debian unstable/main amd64 python3-distutils all 3.8.5-1 [145 kB]
Get:211 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-dev-bin amd64 2.66.0-2 [176 kB]
Get:212 http://debian.oregonstate.edu/debian unstable/main arm64 libsepol1 arm64 3.1-1 [244 kB]
Get:213 http://debian.oregonstate.edu/debian unstable/main arm64 libsepol1-dev arm64 3.1-1 [329 kB]
Get:214 http://debian.oregonstate.edu/debian unstable/main arm64 libpcre2-16-0 arm64 10.34-7 [195 kB]
Get:215 http://debian.oregonstate.edu/debian unstable/main arm64 libpcre2-32-0 arm64 10.34-7 [185 kB]
Get:216 http://debian.oregonstate.edu/debian unstable/main arm64 libpcre2-posix2 arm64 10.34-7 [45.1 kB]
Get:217 http://debian.oregonstate.edu/debian unstable/main arm64 libpcre2-dev arm64 10.34-7 [635 kB]
Get:218 http://debian.oregonstate.edu/debian unstable/main arm64 libselinux1-dev arm64 3.1-2 [170 kB]
Get:219 http://debian.oregonstate.edu/debian unstable/main arm64 libmount-dev arm64 2.36-3+b1 [76.8 kB]
Get:220 http://debian.oregonstate.edu/debian unstable/main arm64 libpcre16-3 arm64 2:8.39-13 [236 kB]
Get:221 http://debian.oregonstate.edu/debian unstable/main arm64 libpcre32-3 arm64 2:8.39-13 [229 kB]
Get:222 http://debian.oregonstate.edu/debian unstable/main arm64 libpcrecpp0v5 arm64 2:8.39-13 [151 kB]
Get:223 http://debian.oregonstate.edu/debian unstable/main arm64 libpcre3-dev arm64 2:8.39-13 [579 kB]
Get:224 http://debian.oregonstate.edu/debian unstable/main amd64 pkg-config amd64 0.29.2-1 [65.1 kB]
Get:225 http://debian.oregonstate.edu/debian unstable/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2 [189 kB]
Get:226 http://debian.oregonstate.edu/debian unstable/main arm64 libglib2.0-dev arm64 2.66.0-2 [1590 kB]
Get:227 http://debian.oregonstate.edu/debian unstable/main amd64 node-jquery all 3.5.1+dfsg-4 [309 kB]
Get:228 http://debian.oregonstate.edu/debian unstable/main amd64 libjs-jquery all 3.5.1+dfsg-4 [3612 B]
Get:229 http://debian.oregonstate.edu/debian unstable/main amd64 libmime-charset-perl all 1.012.2-1 [35.4 kB]
Get:230 http://debian.oregonstate.edu/debian unstable/main amd64 libthai-data all 0.1.28-3 [170 kB]
Get:231 http://debian.oregonstate.edu/debian unstable/main amd64 libthai0 amd64 0.1.28-3 [54.2 kB]
Get:232 http://debian.oregonstate.edu/debian unstable/main amd64 libsombok3 amd64 2.4.0-2+b1 [31.4 kB]
Get:233 http://debian.oregonstate.edu/debian unstable/main arm64 libstdc++-9-dev arm64 9.3.0-18 [1661 kB]
Get:234 http://debian.oregonstate.edu/debian unstable/main amd64 libunicode-linebreak-perl amd64 0.0.20190101-1+b2 [103 kB]
Get:235 http://debian.oregonstate.edu/debian unstable/main amd64 xfonts-encodings all 1:1.0.4-2 [574 kB]
Get:236 http://debian.oregonstate.edu/debian unstable/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB]
Get:237 http://debian.oregonstate.edu/debian unstable/main amd64 lmodern all 2.004.5-6 [9488 kB]
Get:238 http://debian.oregonstate.edu/debian unstable/main amd64 texlive-latex-base all 2020.20200804-3 [1067 kB]
Get:239 http://debian.oregonstate.edu/debian unstable/main amd64 texlive-luatex all 2020.20200804-3 [13.1 MB]
Get:240 http://debian.oregonstate.edu/debian unstable/main amd64 texlive-plain-generic all 2020.20200804-3 [26.3 MB]
Get:241 http://debian.oregonstate.edu/debian unstable/main amd64 texlive-extra-utils all 2020.20200804-3 [55.0 MB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libexpat1:amd64 (2.2.9-1) ...
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Setting up python3-minimal (3.8.2-3) ...
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Setting up libstdc++-9-dev:arm64 (9.3.0-18) ...
Setting up libpcre2-dev:arm64 (10.34-7) ...
Setting up libselinux1-dev:arm64 (3.1-2) ...
Setting up libglib2.0-0:arm64 (2.66.0-2) ...
/var/lib/dpkg/info/libglib2.0-0:arm64.postinst: 47: /usr/lib/aarch64-linux-gnu/glib-2.0/glib-compile-schemas: Exec format error
/var/lib/dpkg/info/libglib2.0-0:arm64.postinst: 50: /usr/lib/aarch64-linux-gnu/glib-2.0/gio-querymodules: Exec format error
Setting up libmount-dev:arm64 (2.36-3+b1) ...
Setting up libglib2.0-dev:arm64 (2.66.0-2) ...
Processing triggers for libc-bin (2.31-3) ...
Processing triggers for sgml-base (1.30) ...
Setting up sgml-data (2.0.11) ...
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:arm64 (0.invalid.0) ...
Processing triggers for tex-common (6.15) ...
Running updmap-sys. This may take some time... done.
Running mktexlsr /var/lib/texmf ... done.
Building format(s) --all.
	This may take some time... done.

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (arm64 included in any all)

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

Kernel: Linux 4.19.0-10-amd64 #1 SMP Debian 4.19.132-1 (2020-07-24) amd64 (x86_64)
Toolchain package versions: binutils_2.35.1-1 dpkg-dev_1.20.5 g++-10_10.2.0-9 gcc-10_10.2.0-9 libc6-dev_2.31-3 libstdc++-10-dev_10.2.0-9 libstdc++-10-dev-arm64-cross_10.2.0-9cross1 libstdc++-9-dev_9.3.0-18 libstdc++6_10.2.0-9 libstdc++6-arm64-cross_10.2.0-9cross1 linux-libc-dev_5.8.10-1
Package versions: adduser_3.118 apt_2.1.10 autoconf_2.69-11.1 automake_1:1.16.2-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.47 bash_5.0-7 binutils_2.35.1-1 binutils-aarch64-linux-gnu_2.35.1-1 binutils-common_2.35.1-1 binutils-x86-64-linux-gnu_2.35.1-1 bsdextrautils_2.36-3+b1 bsdutils_1:2.36-3+b1 build-essential_12.8 bzip2_1.0.8-4 coreutils_8.32-4+b1 cpp_4:10.2.0-1 cpp-10_10.2.0-9 cpp-10-aarch64-linux-gnu_10.2.0-9cross1 cpp-8_8.4.0-4 cpp-aarch64-linux-gnu_4:10.2.0-1 cross-config_2.6.15-3.1 crossbuild-essential-arm64_12.8 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2.1 debian-archive-keyring_2019.1 debianutils_4.11.1 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 docbook_4.5-6 docbook-to-man_1:2.0.0-45 dpkg_1.20.5 dpkg-cross_2.6.15-3.1 dpkg-dev_1.20.5 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.25.1-1 fdisk_2.36-3+b1 file_1:5.38-5 findutils_4.7.0-1 fontconfig-config_2.13.1-4.2 fonts-dejavu-core_2.37-2 fonts-lmodern_2.004.5-6 fonts-urw-base35_20200910-1 g++_4:10.2.0-1 g++-10_10.2.0-9 g++-10-aarch64-linux-gnu_10.2.0-9cross1 g++-aarch64-linux-gnu_4:10.2.0-1 gcc_4:10.2.0-1 gcc-10_10.2.0-9 gcc-10-aarch64-linux-gnu_10.2.0-9cross1 gcc-10-aarch64-linux-gnu-base_10.2.0-9cross1 gcc-10-base_10.2.0-9 gcc-10-cross-base_10.2.0-9cross1 gcc-8-base_8.4.0-4 gcc-9-base_9.3.0-18 gcc-aarch64-linux-gnu_4:10.2.0-1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 ghostscript_9.53.1~dfsg-2 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hevea_2.34-2 hostname_3.23 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libapt-pkg5.0_1.8.4 libapt-pkg6.0_2.1.10 libarchive-zip-perl_1.68-1 libasan5_9.3.0-18 libasan6_10.2.0-9 libasan6-arm64-cross_10.2.0-9cross1 libatomic1_10.2.0-9 libatomic1-arm64-cross_10.2.0-9cross1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3+b1 libavahi-client3_0.8-3 libavahi-common-data_0.8-3 libavahi-common3_0.8-3 libbinutils_2.35.1-1 libblkid-dev_2.36-3+b1 libblkid1_2.36-3+b1 libbrotli1_1.0.9-2 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-4 libc-bin_2.31-3 libc-dev-bin_2.31-3 libc6_2.31-3 libc6-arm64-cross_2.31-1cross2 libc6-dev_2.31-3 libc6-dev-arm64-cross_2.31-1cross2 libcairo2_1.16.0-4 libcap-ng0_0.7.9-2.2 libcc1-0_10.2.0-9 libcom-err2_1.45.6-1 libconfig-auto-perl_0.44-1 libconfig-inifiles-perl_3.000003-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.1-1 libctf0_2.35.1-1 libcups2_2.3.3-3 libdatrie1_0.2.12-3 libdb5.3_5.3.28+dfsg1-0.6 libdbus-1-3_1.12.20-1 libdebconfclient0_0.254 libdebhelper-perl_13.2.1 libdebian-dpkgcross-perl_2.6.15-3.1 libdpkg-perl_1.20.5 libelf1_0.181-1 libexpat1_2.2.9-1 libext2fs2_1.45.6-1 libfakeroot_1.25.1-1 libfdisk1_2.36-3+b1 libffi-dev_3.3-4 libffi6_3.2.1-9 libffi7_3.3-4 libfile-homedir-perl_1.004-1 libfile-stripnondeterminism-perl_1.9.0-1 libfile-which-perl_1.23-1 libfontconfig1_2.13.1-4.2 libfontenc1_1:1.1.4-1 libfreetype6_2.10.2+dfsg-3 libgcc-10-dev_10.2.0-9 libgcc-10-dev-arm64-cross_10.2.0-9cross1 libgcc-9-dev_9.3.0-18 libgcc-s1_10.2.0-9 libgcc-s1-arm64-cross_10.2.0-9cross1 libgcrypt20_1.8.6-2 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libglib2.0-0_2.66.0-2 libglib2.0-bin_2.66.0-2 libglib2.0-data_2.66.0-2 libglib2.0-dev_2.66.0-2 libglib2.0-dev-bin_2.66.0-2 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.15-4 libgomp1_10.2.0-9 libgomp1-arm64-cross_10.2.0-9cross1 libgpg-error0_1.38-2 libgraphite2-3_1.3.14-1 libgs9_9.53.1~dfsg-2 libgs9-common_9.53.1~dfsg-2 libgssapi-krb5-2_1.17-10 libharfbuzz0b_2.6.7-1 libhogweed4_3.5.1+really3.4.1-1 libhogweed6_3.6-2 libice6_2:1.0.10-1 libicu67_67.1-4 libidn11_1.33-2.4 libidn2-0_2.3.0-1 libijs-0.35_0.35-15 libio-string-perl_1.08-3 libisl19_0.20-2 libisl22_0.22.1-1 libitm1_10.2.0-9 libitm1-arm64-cross_10.2.0-9cross1 libjbig0_2.1-3.1+b2 libjbig2dec0_0.19-1 libjpeg62-turbo_1:2.0.5-1.1 libjs-jquery_3.5.1+dfsg-4 libk5crypto3_1.17-10 libkeyutils1_1.6.1-2 libkpathsea6_2020.20200327.54578-5 libkrb5-3_1.17-10 libkrb5support0_1.17-10 liblcms2-2_2.9-4+b1 liblocale-gettext-perl_1.07-4 liblsan0_10.2.0-9 liblsan0-arm64-cross_10.2.0-9cross1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1+b1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmime-charset-perl_1.012.2-1 libmount-dev_2.36-3+b1 libmount1_2.36-3+b1 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libmpx2_8.4.0-4 libncursesw6_6.2+20200918-1 libnetpbm10_2:10.0-15.3+b2 libnettle6_3.5.1+really3.4.1-1 libnettle8_3.6-2 libopenjp2-7_2.3.1-1 libosp5_1.5.2-13+b1 libp11-kit0_0.23.21-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpaper-utils_1.1.28+b1 libpaper1_1.1.28+b1 libpcre16-3_2:8.39-13 libpcre2-16-0_10.34-7 libpcre2-32-0_10.34-7 libpcre2-8-0_10.34-7 libpcre2-dev_10.34-7 libpcre2-posix2_10.34-7 libpcre3_2:8.39-13 libpcre3-dev_2:8.39-13 libpcre32-3_2:8.39-13 libpcrecpp0v5_2:8.39-13 libperl5.28_5.28.1-6 libperl5.30_5.30.3-4 libpipeline1_1.5.3-1 libpixman-1-0_0.36.0-1 libpng16-16_1.6.37-3 libptexenc1_2020.20200327.54578-5 libpython3-stdlib_3.8.2-3 libpython3.8-minimal_3.8.6~rc1-2 libpython3.8-stdlib_3.8.6~rc1-2 libquadmath0_10.2.0-9 libreadline8_8.0-4 libseccomp2_2.4.4-1 libselinux1_3.1-2 libselinux1-dev_3.1-2 libsemanage-common_3.1-1 libsemanage1_3.1-1 libsepol1_3.1-1 libsepol1-dev_3.1-1 libsigsegv2_2.12-2 libsm6_2:1.2.3-1 libsmartcols1_2.36-3+b1 libsombok3_2.4.0-2+b1 libsqlite3-0_3.33.0-1 libss2_1.45.6-1 libssl1.1_1.1.1g-1 libstdc++-10-dev_10.2.0-9 libstdc++-10-dev-arm64-cross_10.2.0-9cross1 libstdc++-9-dev_9.3.0-18 libstdc++6_10.2.0-9 libstdc++6-arm64-cross_10.2.0-9cross1 libsub-override-perl_0.09-2 libsynctex2_2020.20200327.54578-5 libsystemd0_246.6-1 libtasn1-6_4.16.0-2 libteckit0_2.5.10+ds1-3 libtexlua53_2020.20200327.54578-5 libtexluajit2_2020.20200327.54578-5 libthai-data_0.1.28-3 libthai0_0.1.28-3 libtiff5_4.1.0+git191117-2 libtinfo6_6.2+20200918-1 libtool_2.4.6-14 libtsan0_10.2.0-9 libtsan0-arm64-cross_10.2.0-9cross1 libubsan1_10.2.0-9 libubsan1-arm64-cross_10.2.0-9cross1 libuchardet0_0.0.7-1 libudev1_246.6-1 libunicode-linebreak-perl_0.0.20190101-1+b2 libunistring2_0.9.10-4 libuuid1_2.36-3+b1 libwebp6_0.6.1-2+b1 libx11-6_2:1.6.12-1 libx11-data_2:1.6.12-1 libxau6_1:1.0.8-1+b2 libxaw7_2:1.0.13-1+b2 libxcb-render0_1.14-2 libxcb-shm0_1.14-2 libxcb1_1.14-2 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxi6_2:1.7.10-1 libxml-libxml-perl_2.0134+dfsg-2 libxml-namespacesupport-perl_1.12-1 libxml-sax-base-perl_1.09-1 libxml-sax-perl_1.02+dfsg-1 libxml-simple-perl_2.25-1 libxml2_2.9.10+dfsg-6 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 libyaml-perl_1.30-1 libzstd1_1.4.5+dfsg-4 libzzip-0-13_0.13.62-3.2 linux-libc-dev_5.8.10-1 linux-libc-dev-arm64-cross_5.7.6-1cross2 lmodern_2.004.5-6 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0 m4_1.4.18-4 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mime-support_3.64 mount_2.36-3+b1 ncurses-base_6.2+20200918-1 ncurses-bin_6.2+20200918-1 netpbm_2:10.0-15.3+b2 node-jquery_3.5.1+dfsg-4 opensp_1.5.2-13+b1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.28_5.28.1-6 perl-modules-5.30_5.30.3-4 pkg-config_0.29.2-1 po-debconf_1.0.21 poppler-data_0.4.9-2 python3_3.8.2-3 python3-distutils_3.8.5-1 python3-lib2to3_3.8.5-1 python3-minimal_3.8.2-3 python3.8_3.8.6~rc1-2 python3.8-minimal_3.8.6~rc1-2 readline-common_8.0-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sgml-base_1.30 sgml-data_2.0.11 sysvinit-utils_2.96-5 t1utils_1.41-4 tar_1.30+dfsg-7 tex-common_6.15 texlive-base_2020.20200804-3 texlive-binaries_2020.20200327.54578-5 texlive-extra-utils_2020.20200804-3 texlive-latex-base_2020.20200804-3 texlive-luatex_2020.20200804-3 texlive-plain-generic_2020.20200804-3 tzdata_2020a-1 ucf_3.0043 util-linux_2.36-3+b1 uuid-dev_2.36-3+b1 x11-common_1:7.7+20 xdg-utils_1.1.3-2 xfonts-encodings_1:1.0.4-2 xfonts-utils_1:7.7+6 xml-core_0.18+nmu1 xz-utils_5.2.4-1+b1 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.5dfW0Ii_/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

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

APT_CONFIG=/var/lib/sbuild/apt.conf
CONFIG_SITE=/etc/dpkg-cross/cross-config.arm64
DEB_BUILD_OPTIONS=nocheck
HOME=/sbuild-nonexistent
LANG=en_US.UTF-8
LC_ALL=C.UTF-8
LOGNAME=helmut
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=unstable-amd64-sbuild
SCHROOT_CHROOT_NAME=unstable-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1003
SCHROOT_GROUP=helmut
SCHROOT_SESSION_ID=unstable-amd64-sbuild-5777e886-b1bb-4245-b2a2-d6af2869b23a
SCHROOT_UID=1003
SCHROOT_USER=helmut
SHELL=/bin/sh
USER=helmut

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

Command: dpkg-buildpackage -aarm64 -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1
dpkg-buildpackage: info: source package wise
dpkg-buildpackage: info: source version 2.4.1-23
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Helmut Grohne <helmut@subdivi.de>
dpkg-architecture: warning: specified GNU system type aarch64-linux-gnu does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
 debian/rules clean
dh clean
   debian/rules override_dh_clean
make[1]: Entering directory '/<<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=aarch64-linux-gnu-pkg-config CXX=aarch64-linux-gnu-g\+\+ CC=aarch64-linux-gnu-gcc all
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
(cd base   ; make CC="aarch64-linux-gnu-gcc" CFLAGS="-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  `aarch64-linux-gnu-pkg-config --cflags glib-2.0`" libwisebase.a )
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/base'
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include wiseconfig.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include wisestring.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include wiseerror.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include wisememman.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include wisefile.c
wisefile.dy: In function ‘Wise2_myfclose’:
wisefile.dy:72:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘FILE *’ [-Wformat=]
   72 |   fprintf(stderr,"Closing %d\n",ofp);
      |                  ^~~~~~~~~~~~~~ ~~~
      |                                 |
      |                                 FILE *
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include wiserandom.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include wisetime.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include wiseoverlay.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include wisestreaminterface.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include commandline.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include linesubs.c
ar ru libwisebase.a wiseconfig.o wisestring.o wiseerror.o wisememman.o wisefile.o wiserandom.o wisetime.o wiseoverlay.o wisestreaminterface.o commandline.o linesubs.o
ar: `u' modifier ignored since `D' is the default (see `U')
ar: creating libwisebase.a
if test -x /bin/ranlib; then /bin/ranlib libwisebase.a; else exit 0; fi
if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisebase.a; else exit 0; fi
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/base'
(cd HMMer2 ; make CC="aarch64-linux-gnu-gcc" CFLAGS="-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  `aarch64-linux-gnu-pkg-config --cflags glib-2.0`" libhmmer.a )
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/HMMer2'
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c alphabet.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c core_algorithms.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c debug.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c emit.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c emulation.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c histogram.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c hmmio.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c mathsupport.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c masks.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c misc.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c modelmakers.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c plan7.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c plan9.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c prior.c		
prior.c: In function ‘P7ReadPrior’:
prior.c:102:12: warning: implicit declaration of function ‘strcmp’ [-Wimplicit-function-declaration]
  102 |   if      (strcmp(sptr, "DIRICHLET") == 0) pri->strategy = PRI_DCHLET;
      |            ^~~~~~
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c tophits.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c trace.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c aligneval.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c alignio.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c cluster.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c dayhoff.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c file.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c getopt.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c gnuregex.c		
gnuregex.c: In function ‘re_match_2’:
gnuregex.c:3752:31: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 3752 |                           if ((int) old_regend[r] >= (int) regstart[r])
      |                               ^
gnuregex.c:3752:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 3752 |                           if ((int) old_regend[r] >= (int) regstart[r])
      |                                                      ^
gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
 2315 |   fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
      |                                          ^
gnuregex.c:2394:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
 2394 |     PUSH_FAILURE_ITEM (lowest_active_reg);    \
      |     ^~~~~~~~~~~~~~~~~
gnuregex.c:3758:19: note: in expansion of macro ‘PUSH_FAILURE_POINT’
 3758 |                   PUSH_FAILURE_POINT (p1 + mcnt, d, -2);
      |                   ^~~~~~~~~~~~~~~~~~
gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
 2315 |   fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
      |                                          ^
gnuregex.c:2397:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
 2397 |     PUSH_FAILURE_ITEM (highest_active_reg);    \
      |     ^~~~~~~~~~~~~~~~~
gnuregex.c:3758:19: note: in expansion of macro ‘PUSH_FAILURE_POINT’
 3758 |                   PUSH_FAILURE_POINT (p1 + mcnt, d, -2);
      |                   ^~~~~~~~~~~~~~~~~~
gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
 2315 |   fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
      |                                          ^
gnuregex.c:2394:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
 2394 |     PUSH_FAILURE_ITEM (lowest_active_reg);    \
      |     ^~~~~~~~~~~~~~~~~
gnuregex.c:3905:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’
 3905 |           PUSH_FAILURE_POINT (p + mcnt, NULL, -2);
      |           ^~~~~~~~~~~~~~~~~~
gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
 2315 |   fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
      |                                          ^
gnuregex.c:2397:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
 2397 |     PUSH_FAILURE_ITEM (highest_active_reg);    \
      |     ^~~~~~~~~~~~~~~~~
gnuregex.c:3905:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’
 3905 |           PUSH_FAILURE_POINT (p + mcnt, NULL, -2);
      |           ^~~~~~~~~~~~~~~~~~
gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
 2315 |   fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
      |                                          ^
gnuregex.c:2394:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
 2394 |     PUSH_FAILURE_ITEM (lowest_active_reg);    \
      |     ^~~~~~~~~~~~~~~~~
gnuregex.c:3958:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’
 3958 |           PUSH_FAILURE_POINT (p + mcnt, d, -2);
      |           ^~~~~~~~~~~~~~~~~~
gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
 2315 |   fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
      |                                          ^
gnuregex.c:2397:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
 2397 |     PUSH_FAILURE_ITEM (highest_active_reg);    \
      |     ^~~~~~~~~~~~~~~~~
gnuregex.c:3958:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’
 3958 |           PUSH_FAILURE_POINT (p + mcnt, d, -2);
      |           ^~~~~~~~~~~~~~~~~~
gnuregex.c:2482:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 2482 |   high_reg = (unsigned) POP_FAILURE_ITEM ();    \
      |              ^
gnuregex.c:4064:13: note: in expansion of macro ‘POP_FAILURE_POINT’
 4064 |             POP_FAILURE_POINT (sdummy, pdummy,
      |             ^~~~~~~~~~~~~~~~~
gnuregex.c:2485:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 2485 |   low_reg = (unsigned) POP_FAILURE_ITEM ();    \
      |             ^
gnuregex.c:4064:13: note: in expansion of macro ‘POP_FAILURE_POINT’
 4064 |             POP_FAILURE_POINT (sdummy, pdummy,
      |             ^~~~~~~~~~~~~~~~~
gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
 2315 |   fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
      |                                          ^
gnuregex.c:2394:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
 2394 |     PUSH_FAILURE_ITEM (lowest_active_reg);    \
      |     ^~~~~~~~~~~~~~~~~
gnuregex.c:4097:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’
 4097 |           PUSH_FAILURE_POINT (0, 0, -2);
      |           ^~~~~~~~~~~~~~~~~~
gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
 2315 |   fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
      |                                          ^
gnuregex.c:2397:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
 2397 |     PUSH_FAILURE_ITEM (highest_active_reg);    \
      |     ^~~~~~~~~~~~~~~~~
gnuregex.c:4097:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’
 4097 |           PUSH_FAILURE_POINT (0, 0, -2);
      |           ^~~~~~~~~~~~~~~~~~
gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
 2315 |   fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
      |                                          ^
gnuregex.c:2394:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
 2394 |     PUSH_FAILURE_ITEM (lowest_active_reg);    \
      |     ^~~~~~~~~~~~~~~~~
gnuregex.c:4110:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’
 4110 |           PUSH_FAILURE_POINT (0, 0, -2);
      |           ^~~~~~~~~~~~~~~~~~
gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
 2315 |   fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
      |                                          ^
gnuregex.c:2397:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
 2397 |     PUSH_FAILURE_ITEM (highest_active_reg);    \
      |     ^~~~~~~~~~~~~~~~~
gnuregex.c:4110:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’
 4110 |           PUSH_FAILURE_POINT (0, 0, -2);
      |           ^~~~~~~~~~~~~~~~~~
gnuregex.c:2482:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 2482 |   high_reg = (unsigned) POP_FAILURE_ITEM ();    \
      |              ^
gnuregex.c:4278:11: note: in expansion of macro ‘POP_FAILURE_POINT’
 4278 |           POP_FAILURE_POINT (d, p,
      |           ^~~~~~~~~~~~~~~~~
gnuregex.c:2485:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 2485 |   low_reg = (unsigned) POP_FAILURE_ITEM ();    \
      |             ^
gnuregex.c:4278:11: note: in expansion of macro ‘POP_FAILURE_POINT’
 4278 |           POP_FAILURE_POINT (d, p,
      |           ^~~~~~~~~~~~~~~~~
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c interleaved.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c iupac.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c msf.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c revcomp.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c selex.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c sqerror.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c sqio.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c sre_ctype.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c sre_math.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c sre_string.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c stack.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c translate.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c types.c		
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include  -c weight.c		
ar rcv  libhmmer.a alphabet.o    core_algorithms.o debug.o	          emit.o emulation.o   histogram.o       hmmio.o           mathsupport.o masks.o       misc.o            modelmakers.o     plan7.o plan9.o       prior.o           tophits.o         trace.o aligneval.o   alignio.o         cluster.o         dayhoff.o file.o        getopt.o          gnuregex.o        interleaved.o iupac.o       msf.o             revcomp.o         selex.o sqerror.o     sqio.o            sre_ctype.o       sre_math.o sre_string.o  stack.o           translate.o       types.o weight.o
a - alphabet.o
a - core_algorithms.o
a - debug.o
a - emit.o
a - emulation.o
a - histogram.o
a - hmmio.o
a - mathsupport.o
a - masks.o
a - misc.o
a - modelmakers.o
a - plan7.o
a - plan9.o
a - prior.o
a - tophits.o
a - trace.o
a - aligneval.o
a - alignio.o
a - cluster.o
a - dayhoff.o
a - file.o
a - getopt.o
a - gnuregex.o
a - interleaved.o
a - iupac.o
a - msf.o
a - revcomp.o
a - selex.o
a - sqerror.o
a - sqio.o
a - sre_ctype.o
a - sre_math.o
a - sre_string.o
a - stack.o
a - translate.o
a - types.o
a - weight.o
if test -x /bin/ranlib; then /bin/ranlib libhmmer.a; else exit 0; fi
if test -x /usr/bin/ranlib; then /usr/bin/ranlib libhmmer.a; else exit 0; fi
if test -x ranlib; then ranlib libhmmer.a; else exit 0; fi
chmod 644 libhmmer.a
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/HMMer2'
(cd dynlibsrc ; make CC="aarch64-linux-gnu-gcc" CFLAGS="-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  `aarch64-linux-gnu-pkg-config --cflags glib-2.0`" libdyna.a )
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/dynlibsrc'
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ packaln.c
packaln.dy: In function ‘Wise2_read_simple_PackAln’:
packaln.dy:88:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   88 |   fgets(buffer,MAXLINE,ifp);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ aln.c
aln.dy: In function ‘Wise2_mapped_ascii_AlnBlock’:
aln.dy:867:19: warning: too many arguments for format [-Wformat-extra-args]
  867 |       fprintf(ofp," {%3.2f}  ",(double)(*score_to_double)(cuml),cuml);
      |                   ^~~~~~~~~~~~
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ dnamatrix.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ probability.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ alnrange.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ alnconvert.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ basematrix.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ shattermatrix.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ matrixdebug.c
matrixdebug.dy: In function ‘Wise2_user_DebugMatrix’:
matrixdebug.dy:208:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  208 |     fgets(buffer,MAXLINE,in);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ dpenvelope.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ dbsearchimpl.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ dprunimpl.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ complexsequence.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ complexevalset.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ complexconsensi.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ sequence.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ sequencestream.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ seqalign.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ hitlist.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ hsp.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ hspstream.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ codon.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ compmat.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ codonmatrix.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ codonmapper.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ sequencedb.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ hscore.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ seqlookup.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ arrayseqlookup.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ genericindexresult.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ linkedlist_lookpos.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ singlenumberspace.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ histogram.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ searchstatinterface.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ searchstatlookup.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ proteindb.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ protein.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ pairbase.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ pairbaseseq.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ genomicdb.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ randommodel.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ randomdb.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ genomic.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ cdna.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ cdnadb.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ dna.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ embl.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ genomicregion.c
genomicregion.dy: In function ‘Wise2_read_EMBL_FT_into_GenomicRegion’:
genomicregion.dy:756:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  756 |   fgets(buffer,maxlen,ifp);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ gene.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ transcript.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ translation.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ btcanvas.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ asciibtcanvas.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ dynlibcross.c
ar ru libdyna.a packaln.o aln.o dnamatrix.o probability.o alnrange.o alnconvert.o basematrix.o shattermatrix.o matrixdebug.o dpenvelope.o dbsearchimpl.o dprunimpl.o complexsequence.o complexevalset.o complexconsensi.o sequence.o sequencestream.o seqalign.o hitlist.o hsp.o hspstream.o codon.o compmat.o codonmatrix.o codonmapper.o sequencedb.o hscore.o seqlookup.o arrayseqlookup.o genericindexresult.o linkedlist_lookpos.o singlenumberspace.o histogram.o searchstatinterface.o searchstatlookup.o proteindb.o protein.o pairbase.o pairbaseseq.o genomicdb.o randommodel.o randomdb.o genomic.o cdna.o cdnadb.o dna.o embl.o genomicregion.o gene.o transcript.o translation.o btcanvas.o asciibtcanvas.o dynlibcross.o
ar: `u' modifier ignored since `D' is the default (see `U')
ar: creating libdyna.a
if test -x /bin/ranlib; then /bin/ranlib libdyna.a; else exit 0; fi
if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna.a; else exit 0; fi
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/dynlibsrc'
(cd dynlibsrc ; make CC="aarch64-linux-gnu-gcc" CFLAGS="-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  `aarch64-linux-gnu-pkg-config --cflags glib-2.0`" libdyna_glib.a )
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/dynlibsrc'
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ subseqhash.c
subseqhash.dy: In function ‘Wise2_is_populated_subseqhash_ghash’:
subseqhash.dy:111:29: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  111 |   if( g_hash_table_lookup(h,(gconstpointer)seq_number) == NULL ) {
      |                             ^
subseqhash.dy: In function ‘Wise2_lookup_subseqhash_ghash’:
subseqhash.dy:128:85: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  128 |   return new_linkedl_SeqLookupResultInterface((SeqLookupPos *)g_hash_table_lookup(h,(gconstpointer)seq_number));
      |                                                                                     ^
subseqhash.dy: In function ‘Wise2_add_seq_subseqhash_ghash’:
subseqhash.dy:160:54: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  160 |     if((ret = (SeqLookupPos *) g_hash_table_lookup(h,(gconstpointer)seq_number)) == NULL ) {
      |                                                      ^
subseqhash.dy:161:29: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  161 |       g_hash_table_insert(h,(gpointer)seq_number,p);
      |                             ^
subseqhash.dy: In function ‘Wise2_add_direct_number_subseqhash_ghash’:
subseqhash.dy:188:52: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  188 |   if((ret = (SeqLookupPos *) g_hash_table_lookup(h,(gconstpointer)seq_number)) == NULL ) {
      |                                                    ^
subseqhash.dy:189:27: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
  189 |     g_hash_table_insert(h,(gpointer)seq_number,p);
      |                           ^
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ intallocator.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ proteinstreamedindex.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ shadowseq.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ shadowseqindex.c
shadowseqindex.dy: In function ‘Wise2_dump_stats_ShadowSequenceIndex’:
shadowseqindex.dy:285:15: warning: format ‘%f’ expects argument of type ‘double’, but argument 4 has type ‘long unsigned int’ [-Wformat=]
  285 |   fprintf(ofp,"Head memory %d [%.2f Mbytes]\n",total_head,(total_head*sizeof(ShadowArraySeqHead))/100000);
      |               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                                                  |
      |                                                                                                  long unsigned int
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ hsphandler.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ hspscaninterface.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ hsp2hitscan.c
hsp2hitscan.dy: In function ‘Wise2_one_off_two_hit_HSPscan_query_direct’:
hsp2hitscan.dy:209:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘__time_t’ {aka ‘long int’} [-Wformat=]
  209 |   fprintf(stderr,"START %d.%03du %d.%03ds \n",
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
  210 |    use.ru_utime.tv_sec,
      |    ~~~~~~~~~~~~~~~~~~~
      |                |
      |                __time_t {aka long int}
hsp2hitscan.dy:209:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘__time_t’ {aka ‘long int’} [-Wformat=]
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=]
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ hsplookupscan.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ hsplookupthreaded.c
hsplookupthreaded.dy: In function ‘Wise2_one_off_ordered_HSPscan_scan_query_direct’:
hsplookupthreaded.dy:263:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=]
  263 |   fprintf(stderr,"retrieved array with %d elements\n",current_oph);
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~
      |                                                       |
      |                                                       long int
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ hspthreadeddb.c
hspthreadeddb.dy: In function ‘Wise2_threadeddb_scan_worker’:
hspthreadeddb.dy:154:77: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  154 |   fprintf(stderr,"For segment %d, finished query with %d (%d) linear\n",seg,(int)seg->lm,seg->lm->len);
      |                                                                             ^
hspthreadeddb.dy:154:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Wise2_HSPDatabaseSegment *’ [-Wformat=]
  154 |   fprintf(stderr,"For segment %d, finished query with %d (%d) linear\n",seg,(int)seg->lm,seg->lm->len);
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~
      |                                                                         |
      |                                                                         Wise2_HSPDatabaseSegment *
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ hspscanruntime.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ hsptwohitscan.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ proteinindexcons.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ dnaindexcons.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ staticseq.c
ar ru libdyna_glib.a subseqhash.o intallocator.o proteinstreamedindex.o shadowseq.o shadowseqindex.o hsphandler.o hspscaninterface.o hsp2hitscan.o hsplookupscan.o hsplookupthreaded.o hspthreadeddb.o hspscanruntime.o hsptwohitscan.o proteinindexcons.o dnaindexcons.o staticseq.o
ar: `u' modifier ignored since `D' is the default (see `U')
ar: creating libdyna_glib.a
if test -x /bin/ranlib; then /bin/ranlib libdyna_glib.a; else exit 0; fi
if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna_glib.a; else exit 0; fi
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/dynlibsrc'
(cd external ;  make CC="aarch64-linux-gnu-gcc" CFLAGS="-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  `aarch64-linux-gnu-pkg-config --cflags glib-2.0`" all )
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/external'
(cd mott; make CC="aarch64-linux-gnu-gcc" CFLAGS="-g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include" all)
make[4]: Entering directory '/<<PKGBUILDDIR>>/src/external/mott'
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -Wdate-time -D_FORTIFY_SOURCE=2  -c -o mott_api.o mott_api.c
mott_api.c: In function ‘InitPvaluesMott’:
mott_api.c:64:3: warning: implicit declaration of function ‘free’ [-Wimplicit-function-declaration]
   64 |   free(freq0);
      |   ^~~~
mott_api.c: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’
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -Wdate-time -D_FORTIFY_SOURCE=2  -c -o gaplib.o gaplib.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../../dynlibsrc -I../../base wise2_mott_bridge.c
ar ru libmott.a mott_api.o gaplib.o wise2_mott_bridge.o
ar: `u' modifier ignored since `D' is the default (see `U')
ar: creating libmott.a
if test -x /bin/ranlib; then /bin/ranlib libmott.a; else exit 0; fi
if test -x /usr/bin/ranlib; then /usr/bin/ranlib libmott.a; else exit 0; fi
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src/external/mott'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/external'
(cd socket ; make CC="aarch64-linux-gnu-gcc" CFLAGS="-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  `aarch64-linux-gnu-pkg-config --cflags glib-2.0`" libwisesocket.a )
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/socket'
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-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);
      |  ^~~~~~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ functionclient.c
functionclient.dy: In function ‘Wise2_new_FunctionProxyCoordinator’:
functionclient.dy:193:24: warning: passing argument 2 of ‘connect’ from incompatible pointer type [-Wincompatible-pointer-types]
  193 |   connect(out->socket, &server, sizeof(server));
      |                        ^~~~~~~
      |                        |
      |                        struct sockaddr_in *
In file included from functionclient.c:7:
/usr/aarch64-linux-gnu/include/sys/socket.h:126:52: note: expected ‘const struct sockaddr *’ but argument is of type ‘struct sockaddr_in *’
  126 | extern int connect (int __fd, __CONST_SOCKADDR_ARG __addr, socklen_t __len);
      |                                                    ^
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ anonobj.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ transferinterface.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ directsocketwrite.c
ar ru libwisesocket.a functionserver.o functionclient.o anonobj.o transferinterface.o directsocketwrite.o
ar: `u' modifier ignored since `D' is the default (see `U')
ar: creating libwisesocket.a
if test -x /bin/ranlib; then /bin/ranlib libwisesocket.a; else exit 0; fi
if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisesocket.a; else exit 0; fi
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/socket'
(cd dnaindex ; make CC="aarch64-linux-gnu-gcc" CFLAGS="-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  `aarch64-linux-gnu-pkg-config --cflags glib-2.0`" all )
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/dnaindex'
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly.c
kmer_assembly.dy: In function ‘Wise2_show_KmerAssemblyNode’:
kmer_assembly.dy:296:15: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=]
  296 |   fprintf(ofp,"Node %ld of sequence %s \n",node->number,buffer);
      |               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~
      |                                                |
      |                                                kmer_t {aka long long int}
kmer_assembly.dy:302:17: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=]
  302 |     fprintf(ofp,"  ... prev ... %c, %d to %ld\n",node->prev[i]->base,node->prev[i]->sequence_label_len,node->prev[i]->prev->number);
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                                                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                                                                           |
      |                                                                                                                           kmer_t {aka long long int}
kmer_assembly.dy:309:17: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 5 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=]
  309 |     fprintf(ofp,"  ... next ... %c, %d to %ld\n",node->next[i]->base,node->next[i]->sequence_label_len,node->next[i]->next->number);
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                                                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                                                                           |
      |                                                                                                                           kmer_t {aka long long int}
kmer_assembly.dy: In function ‘Wise2_remove_sequence_label_KmerAssemblyLink’:
kmer_assembly.dy:365:18: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘KmerAssemblyLink *’ [-Wformat=]
  365 |   fprintf(stderr,"    ...unable to remove label %ld from link %ld (%d labels)\n",label,kal,kal->sequence_label_len);
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~       ~~~
      |                                                                                        |
      |                                                                                        KmerAssemblyLink *
kmer_assembly.dy:367:20: warning: format ‘%d’ expects a matching ‘int’ argument [-Wformat=]
  367 |     fprintf(stderr,"     [%ld] is %d label\n",kal->sequence_label[i]);
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_index_interface.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_direct.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_hash.c
kmer_hash.dy: In function ‘Wise2_free_KmerHashIndex’:
kmer_hash.dy:318:19: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=]
  318 |   fprintf(stderr, "min_kmer: %016lx\n", khi->min_kmer);
      |                   ^~~~~~~~~~~~~~~~~~~~  ~~~~~~~~~~~~~
      |                                            |
      |                                            kmer_t {aka long long int}
kmer_hash.dy:319:19: warning: format ‘%lx’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=]
  319 |   fprintf(stderr, "max_kmer: %016lx\n", khi->max_kmer);
      |                   ^~~~~~~~~~~~~~~~~~~~  ~~~~~~~~~~~~~
      |                                            |
      |                                            kmer_t {aka long long int}
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_count.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_glib_index.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models singleseqspace.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models dnamapping.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models largeseqreader.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_untangler.c
kmer_assembly_untangler.dy: In function ‘Wise2_show_KmerAssemblyPath’:
kmer_assembly_untangler.dy:52:65: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
   52 |     fprintf(ofp,"%3d memory %d, from [%s] to [%s], base %c\n",i,(int)kap->stack[i],back,forw,kap->stack[i]->base);
      |                                                                 ^
kmer_assembly_untangler.dy: In function ‘Wise2_untangle_KmerAssembly’:
kmer_assembly_untangler.dy:120:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=]
  120 |       fprintf(stderr,"TANGLE: Node %ld, %s has forward %d and back %d links\n",node->number,buffer,node->next_len,node->prev_len);
      |                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~
      |                                                                                    |
      |                                                                                    kmer_t {aka long long int}
kmer_assembly_untangler.dy:141:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=]
  141 |       fprintf(stderr,"Will attempt untangle starting at %ld to %ld\n",node->prev[i]->prev->number,node->number);
      |                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                                          |
      |                                                                                          kmer_t {aka long long int}
kmer_assembly_untangler.dy:141:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=]
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=]
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_contig.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_error.c
kmer_assembly_error.dy: In function ‘Wise2_mark_tangles_KmerAssembly’:
kmer_assembly_error.dy:93:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=]
   93 |       fprintf(stderr,"Marking node (%ld) [%s] as next tangled\n",node->number,buffer);
      |                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~
      |                                                                      |
      |                                                                      kmer_t {aka long long int}
kmer_assembly_error.dy:105:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=]
  105 |       fprintf(stderr,"Marking node (%ld) [%s] as prev tangled\n",node->number,buffer);
      |                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~
      |                                                                      |
      |                                                                      kmer_t {aka long long int}
kmer_assembly_error.dy: In function ‘Wise2_extend_indel_path_KmerAssembly’:
kmer_assembly_error.dy:351:17: 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 *
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models compressed_protein_index.c
compressed_protein_index.dy: In function ‘Wise2_add_direct_number_CompressedProteinIndex’:
compressed_protein_index.dy:223:10: warning: returning ‘void *’ from a function with return type ‘boolean’ {aka ‘int’} makes integer from pointer without a cast [-Wint-conversion]
  223 |   return NULL;
      |          ^~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/dnaindex'
(cd network ; make  CC="aarch64-linux-gnu-gcc" CFLAGS="-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  `aarch64-linux-gnu-pkg-config --cflags glib-2.0`" all )
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/network'
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/  -I../socket -I../dynlibsrc -I../dnaindex wise_proteinindex_server.c
wise_proteinindex_server.c: In function ‘show_version’:
wise_proteinindex_server.c:28:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
   28 |   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
      |                                                                                                       ^~~~~~~~~~~~
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/  -I../socket -I../dynlibsrc -I../dnaindex net_hspscan.c
aarch64-linux-gnu-gcc -g -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o  -ldyna_glib -ldyna -lwisesocket -lwisebase -Wl,-z,relro -Wl,-z,now -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `aarch64-linux-gnu-pkg-config --libs glib-2.0` -lpthread 
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-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="aarch64-linux-gnu-gcc" CFLAGS="-g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c  `aarch64-linux-gnu-pkg-config --cflags glib-2.0`" EXTRALIBS="-lm" HMMER_DEFINE="HMMER_INTERNAL" HMMER_INCLUDE="../HMMer2/" HMMER_LIBS="../HMMer2/" all )
make[3]: Entering directory '/<<PKGBUILDDIR>>/src/models'
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dnal.c
dnal.c: In function ‘show_version’:
dnal.c:106:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
  106 |   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
      |                                                                                                       ^~~~~~~~~~~~
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dnaalign.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ seqaligndisplay.c
aarch64-linux-gnu-gcc -o dnal dnal.o dnaalign.o seqaligndisplay.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ psw.c
psw.c: In function ‘show_version’:
psw.c:261:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
  261 |   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
      |                                                                                                       ^~~~~~~~~~~~
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ proteinsw.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ sw_wrap.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ abc.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pba.c
aarch64-linux-gnu-gcc -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o   -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pswdb.c
pswdb.c: In function ‘show_version’:
pswdb.c:97:106: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
   97 |   fprintf(stdout,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
      |                                                                                                          ^~~~~~~~~~~~
aarch64-linux-gnu-gcc -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dbac.c
dbac.c: In function ‘show_version’:
dbac.c:364:33: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
  364 |   fprintf(ofp,"  Compiled %s\n",COMPILE_DATE);
      |                                 ^~~~~~~~~~~~
dbac.c: In function ‘make_SeqAlign_from_align’:
dbac.c:413:32: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
  413 |   fprintf(stderr,"Got %d with %d vs %d\n",i,strlen(seq),one->len);
      |                               ~^            ~~~~~~~~~~~
      |                                |            |
      |                                int          size_t {aka long unsigned int}
      |                               %ld
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dba.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ slimdba.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ bigdba.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ dbadisplay.c
aarch64-linux-gnu-gcc -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include estwise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I.
estwise.c: In function ‘show_version’:
estwise.c:559:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
  559 |   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
      |                                                                                                       ^~~~~~~~~~~~
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparser21.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparameter.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genestats.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisehsp.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneutil.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneoutput.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ threestatemodel.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genefrequency.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ splicesitemodeler.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise4.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise6.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genestretch6.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewise21.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneloop21.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneloop6.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genephase6.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ gwlite.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ gwlitemodel.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ gwrap.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ matchsum.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estwrap.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisemodel.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ phasemodel.c
phasemodel.dy: In function ‘Wise2_read_fasta_PhasedProtein’:
phasemodel.dy:241:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  241 |   fgets(name,10000,ifp);
      |   ^~~~~~~~~~~~~~~~~~~~~
In file included from /usr/aarch64-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/aarch64-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);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ cdparser.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genedisplay.c
genedisplay.dy: In function ‘Wise2_write_intron_desc’:
genedisplay.dy:493:20: warning: too many arguments for format [-Wformat-extra-args]
  493 |     sprintf(buffer,"  Intron ???  ",in_number);
      |                    ^~~~~~~~~~~~~~~~
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estwise3.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estslim3.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estloop3.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estfrag3.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estslimloop.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ gwquickdb.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ threestatedb.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pfamhmmer1db.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pwmdna.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../HMMer2/ -DHMMER_INTERNAL -I../base/ -I../dynlibsrc/ wise2xhmmer2.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genewisemodeldb.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ seqhit.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ standardout.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ geneparser4.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ estquick3.c
aarch64-linux-gnu-gcc -g -o estwise estwise.o  geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o  -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase  -lm -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0`
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include genewise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I.
genewise.c: In function ‘show_version’:
genewise.c:860:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
  860 |   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
      |                                                                                                       ^~~~~~~~~~~~
aarch64-linux-gnu-gcc -o genewise genewise.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o  -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase  -lm -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0`
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include genewisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ 
genewisedb.c: In function ‘show_version’:
genewisedb.c:1005:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
 1005 |   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
      |                                                                                                       ^~~~~~~~~~~~
aarch64-linux-gnu-gcc -g -o genewisedb genewisedb.o  geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o   -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase  -lm  -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0`
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include estwisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/
estwisedb.c: In function ‘show_version’:
estwisedb.c:838:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
  838 |   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
      |                                                                                                       ^~~~~~~~~~~~
aarch64-linux-gnu-gcc -g -o estwisedb estwisedb.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o   -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase  -lm -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0`
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genomewise.c
genomewise.c: In function ‘show_version’:
genomewise.c:18:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
   18 |   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
      |                                                                                                       ^~~~~~~~~~~~
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genomewise9.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ genome_evidence.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ est_evidence.c
est_evidence.dy: In function ‘Wise2_new_est_GenomeEvidenceUnit’:
est_evidence.dy:142:16: warning: assignment to ‘int (*)(void *)’ from incompatible pointer type ‘Wise2_EstEvidence * (*)(Wise2_EstEvidence *)’ [-Wincompatible-pointer-types]
  142 |   in->geu_free = free_EstEvidence;
      |                ^
aarch64-linux-gnu-gcc -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ sywise.c
sywise.c: In function ‘show_version’:
sywise.c:14:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
   14 |   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
      |                                                                                                       ^~~~~~~~~~~~
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ sywise20.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ syexonmodel.c
aarch64-linux-gnu-gcc -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o  standardout.o geneutil.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pseudowise.c
pseudowise.c: In function ‘show_version’:
pseudowise.c:15:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
   15 |   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
      |                                                                                                       ^~~~~~~~~~~~
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pseudowise7.c
aarch64-linux-gnu-gcc -g -o pseudowise pseudowise.o pseudowise7.o geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o  -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0` -lhmmer -ldyna_glib -ldyna -lwisebase  -lm -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0`
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ `aarch64-linux-gnu-pkg-config --cflags glib-2.0` promoterwise.c
promoterwise.c: In function ‘show_version’:
promoterwise.c:17:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
   17 |   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
      |                                                                                                       ^~~~~~~~~~~~
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ localdba.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ `aarch64-linux-gnu-pkg-config --cflags glib-2.0` localcishit.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ localcispara.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ motifmatrix.c
motifmatrix.c: In function ‘Wise2_MotifConsMatrix_alloc_matrix’:
motifmatrix.c:408:24: warning: assignment to ‘char’ from ‘void *’ makes integer from pointer without a cast [-Wint-conversion]
  408 |     for(i=0;i<leni;i++)  {
      |                        ^
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ motifmatrixdp.c
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ transfactor.c
transfactor.dy: In function ‘Wise2_read_ben_IUPAC_TransFactorSet’:
transfactor.dy:680:21: warning: ‘%s’ directive writing up to 511 bytes into a region of size between 495 and 504 [-Wformat-overflow=]
  680 |     sprintf(sbuffer,"motif_%d_%s",motif_no,buffer);
      |                     ^~~~~~~~~~~~~          ~~~~~~
In file included from /usr/aarch64-linux-gnu/include/stdio.h:867,
                 from ../base/wisebase.h:6,
                 from pwmdna.h:6,
                 from transfactor.h:6,
                 from transfactor.c:4:
/usr/aarch64-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 ());
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ pairwiseshortdna.c
aarch64-linux-gnu-gcc -g -o promoterwise promoterwise.o localdba.o  localcishit.o localcispara.o dbadisplay.o  motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o  pairwiseshortdna.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm `aarch64-linux-gnu-pkg-config --libs glib-2.0` -lpthread
aarch64-linux-gnu-gcc  -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/  -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c 
scanwisep.c: In function ‘show_version’:
scanwisep.c:423:103: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
  423 |   fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE);
      |                                                                                                       ^~~~~~~~~~~~
aarch64-linux-gnu-gcc -g -O2 -fdebug-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/aarch64-linux-gnu/glib-2.0/include -I../base/ -I../dynlibsrc/ `aarch64-linux-gnu-pkg-config --cflags glib-2.0` hsp2aln_sw.c
aarch64-linux-gnu-gcc -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o   ../network/net_hspscan.o ../network/client_multihspscan.o  -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0` -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase  -lm -lpthread -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `aarch64-linux-gnu-pkg-config --libs glib-2.0`
ar ru libmodel.a geneparser21.o geneparameter.o genestats.o genewisehsp.o geneutil.o geneoutput.o threestatemodel.o genefrequency.o splicesitemodeler.o genewise4.o genewise6.o genestretch6.o genewise21.o geneloop21.o geneloop6.o genephase6.o gwlite.o gwlitemodel.o gwrap.o matchsum.o estwrap.o genewisemodel.o phasemodel.o cdparser.o genedisplay.o estwise3.o estslim3.o estloop3.o estfrag3.o estslimloop.o gwquickdb.o threestatedb.o pfamhmmer1db.o pwmdna.o wise2xhmmer2.o genewisemodeldb.o seqhit.o standardout.o geneparser4.o sw_wrap.o abc.o pba.o seqaligndisplay.o dbadisplay.o proteinsw.o estquick3.o 
ar: `u' modifier ignored since `D' is the default (see `U')
ar: creating libmodel.a
make[3]: Leaving directory '/<<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 <2020-02-02> patch level 5
L3 programming layer <2020-07-17>
(/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 2019/12/20 v1.4l Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))
(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def)
No file api.aux.
(/usr/share/texlive/texmf-dist/tex/latex/base/ulasy.fd) [1{/var/lib/texmf/fonts
/map/pdftex/updmap/pdftex.map}]
No file api.toc.
[2] [3]
Overfull \hbox (1.49698pt too wide) in paragraph at lines 109--109
[]    \OT1/cmtt/m/n/10 print "You must give a file to revcom for a reverse to w
ork!";[] 
[4] [5]

LaTeX Warning: Reference `object_CodonTable' on page 6 undefined on input line 
198.


LaTeX Warning: Reference `object_Sequence' on page 6 undefined on input line 19
9.


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[6]

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ne 233.


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ine 235.


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LaTeX Warning: Reference `module_gwrap' on page 7 undefined on input line 237.


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[]\OT1/cmr/m/n/10 Build an en-tire pa-ram-e-ter set for ge-newise us-ing Wise2:
:GeneParameter21[]wrap

LaTeX Warning: Reference `module_gwrap' on page 7 undefined on input line 238.


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[7] [8] [9]

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[10]

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e 395.


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ne 400.


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ine 401.


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ine 402.


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e 423.


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LaTeX Warning: Reference `module_compmat' on page 11 undefined on input line 42
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e 427.

[11]

LaTeX Warning: Reference `module_hscore' on page 12 undefined on input line 433
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 443.


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e 457.


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464.


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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
[12] (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd)

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e 654.


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[16]

LaTeX Warning: Reference `object_cDNA' on page 17 undefined on input line 741.


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[20]

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LaTeX Warning: Reference `object_CodonMapper' on page 28 undefined on input lin
e 1363.


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[28]
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[]\OT1/cmtt/m/n/10 &Wise2::CodonMapper::sprinkle[]errors[]over[]CodonMapper (cm
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LaTeX Warning: Reference `object_ComplexSequence' on page 29 undefined on input
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n input line 1444.


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[29]

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LaTeX Warning: Reference `object_CompMat' on page 30 undefined on input line 15
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ne 1624.

[32]

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

[34]

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[35]

LaTeX Warning: Reference `object_Gene' on page 36 undefined on input line 1844.



LaTeX Warning: Reference `accessing_fields' on page 36 undefined on input line 
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LaTeX Warning: Reference `object_Genomic' on page 38 undefined on input line 19
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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]

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[44]
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[]\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::read[]EMBL[]GenomicRegion[]file (file
name) 
[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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[]\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::show[]pretty[]GenomicRegion (gr,show[
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[46] [47]

LaTeX Warning: Reference `object_Histogram' on page 48 undefined on input line 
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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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[]\OT1/cmr/m/n/10 should[]store Type [boolean (*should[]store)(int given[]score
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[55] [56] [57]

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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]

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[66]

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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
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[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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\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]

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[81]

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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,ct
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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
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[]\OT1/cmtt/m/n/10 &Wise2::protein2genomic[]ascii[]display (alb,p,gen,ct,name,m
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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 : 
Scalar]

LaTeX Warning: Reference `accessing_fields' on page 88 undefined on input line 
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LaTeX Warning: Reference `object_GeneParameter21' on page 89 undefined on input
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[89]

LaTeX Warning: Reference `object_MatchSummarySet' on page 90 undefined on input
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LaTeX Warning: Reference `object_MatchSummary' on page 90 undefined on input li
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[]\OT1/cmtt/m/n/10 Wise2[]MatchSummarySet[]from[]AlnBlock[]estwise (alb,qname,o
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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
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[90]
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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
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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
put line 5243.


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]

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[]\OT1/cmtt/m/n/10 &Wise2::DnaSequenceHitList::read[]MSPcrunch[]DnaSequenceHitL
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[95]

LaTeX Warning: Reference `accessing_fields' on page 96 undefined on input line 
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[]\OT1/cmtt/m/n/10 Wise2[]Align[]strings[]ProteinSmithWaterman (one,two,comp,ga
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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
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[97]
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[]\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]SmithWaterman (one,two,comp,gap,ext,
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[]\OT1/cmtt/m/n/10 &Wise2::Align[]Proteins[]SmithWaterman (one,two,comp,gap,ext
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[]\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]ABC (one,two,comp,a,b,c,dpenv,dpri) 

[98]
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\OT1/cmr/m/n/10 Align[]Sequences[]ProteinABC this func-tion is anal-o-gous to A
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[99]
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[100]
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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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* tdb,DataEntry

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[105]
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[]\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->force[]weighted[]local[]model(prob[]i
nto[]model,ratio[]start,ratio[]end) 

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[106]
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[]\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->ThreeStateModel[]from[]half[]bit[]Seq
uence(mat,rm,gap,ext) 

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

LaTeX Warning: Reference `accessing_fields' on page 107 undefined on input line
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[107] [108] (./api.aux)
kpathsea: Running mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 tctt1000
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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 <2020-02-02> patch level 5
L3 programming layer <2020-07-17>
(/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 2019/12/20 v1.4l Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))
(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdfmode.def)
(./api.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ulasy.fd) [1{/var/lib
/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./api.toc [2] [3] [4] [5] [6]
[7] [8] [9]) [10] [11]
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[]    \OT1/cmtt/m/n/10 print "You must give a file to revcom for a reverse to w
ork!";[] 
[12] [13] [14]

LaTeX Warning: Reference `object_GeneFrequency' on page 15 undefined on input l
ine 233.


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[]\OT1/cmr/m/n/10 Build an en-tire pa-ram-e-ter set for ge-newise us-ing Wise2:
:GeneParameter21[]wrap

LaTeX Warning: Reference `module_gwrap' on page 15 undefined on input line 238.



LaTeX Warning: Reference `module_gwrap' on page 15 undefined on input line 239.


[15] [16] [17]

LaTeX Warning: Reference `module_gwrap' on page 18 undefined on input line 389.


[18]

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26.

[19]

LaTeX Warning: Reference `module_dbimpl' on page 20 undefined on input line 435
.


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\OT1/cmr/m/n/10 AlnBlock is the main rep-re-sen-ta-tion of align-ments from Dy-
na-mite. Each AlnBlock
[20] (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmtt.fd) [21] [22]
[23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36]
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[]\OT1/cmtt/m/n/10 &Wise2::CodonMapper::sprinkle[]errors[]over[]CodonMapper (cm
,error) 
[37] [38] [39] [40] [41] [42] [43] [44] [45] [46]
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[]\OT1/cmtt/m/n/10 Wise2[]Genomic[]from[]Sequence[]Nheuristic (seq,length[]of[]
N) 
[47] [48] [49]
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[]\OT1/cmtt/m/n/10 Wise2[]new[]GenomicDB[]from[]single[]seq (gen,cses,score[]in
[]repeat[]coding) 

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

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

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

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

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

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

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[]\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->set[]EVD(mu,lambda,lowbound,highbound
,wonka,ndegrees) 
[60] [61] [62]
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[]\OT1/cmr/m/n/10 should[]store Type [boolean (*should[]store)(int given[]score
,double in-ter-nal[]score[]level)
[63] [64] [65] [66] [67] [68] [69] [70] [71] [72] [73] [74] [75] [76]
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[]\OT1/cmtt/m/n/10 Wise2[]force[]to[]dna[]Sequence (seq,fraction,number[]of[]co
nver) 
[77] [78] [79] [80] [81] [82] [83] [84] [85] [86] [87]
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\OT1/cmr/m/n/10 have any se-quence in it. When se-quence is asked for by get[]P
rotein[]from[]Translation()
[88] [89]
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[]\OT1/cmtt/m/n/10 Wise2[]make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap,
text,dpri) 

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[]\OT1/cmtt/m/n/10 &Wise2::make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap
,text,dpri) 
[90]
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[]\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]TSM[]estwise (tdb,cdb,cp,cm,rmd,use[]sy
n,alg,bits[]cutoff,allN,flat[]insert,report[]level,die[]on[]error,dbsi) 

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[]\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]TSM[]estwise (tdb,cdb,cp,cm,rmd,use[]s
yn,alg,bits[]cutoff,allN,flat[]insert,report[]level,die[]on[]error,dbsi) 
[91]
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[]\OT1/cmtt/m/n/10 Wise2[]AlnBlock[]from[]Protein[]estwise[]wrap (pro,cdna,cp,c
m,ct,comp,gap,ext,is[]global,rmd,alg,rm,use[]syn,allN,dpri,palpoi) 

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[]\OT1/cmtt/m/n/10 &Wise2::AlnBlock[]from[]Protein[]estwise[]wrap (pro,cdna,cp,
cm,ct,comp,gap,ext,is[]global,rmd,alg,rm,use[]syn,allN,dpri) 
[92]
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[]\OT1/cmtt/m/n/10 Wise2[]AlnBlock[]from[]TSM[]estwise[]wrap (tsm,cdna,cp,cm,ct
,rmd,alg,use[]syn,force[]flat[]insert,allN,dpri,palpoi) 

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[]\OT1/cmtt/m/n/10 &Wise2::AlnBlock[]from[]TSM[]estwise[]wrap (tsm,cdna,cp,cm,c
t,rmd,alg,use[]syn,force[]flat[]insert,allN,dpri) 
[93]
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[]\OT1/cmtt/m/n/10 Wise2[]protein2genomic[]ascii[]display (alb,p,gen,ct,name,ma
in,ofp) 

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

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

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

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

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newise

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

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

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

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

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[]\OT1/cmr/m/n/10 [OWNER] new AlnBlock struc-ture rep-re-sent-ing the align-men
t [AlnBlock
[105]
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[]\OT1/cmtt/m/n/10 Wise2[]Align[]Proteins[]SmithWaterman (one,two,comp,gap,ext,
dpenv,dpri) 

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

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

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

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

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

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

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

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[]\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b,
c,bits[]cutoff,report[]level,die[]on[]error,dbsi) 
[108]
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[]\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinBA (querydb,targetdb,comp,bentry
,bexit,bfor[]trans,b[]self[]trans,b3exit,bits[]cutoff,report[]level,dbsi) 

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[]\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinBA (querydb,targetdb,comp,bentr
y,bexit,bfor[]trans,b[]self[]trans,b3exit,bits[]cutoff,report[]level,dbsi) 
[109]
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[]\OT1/cmr/m/n/10 reload[]generic Type [Three-State-Model * (*reload[]generic)(
ThreeStateDB * tdb,int

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

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[]\OT1/cmr/m/n/10 index[]generic Type [Three-State-Model * (*in-dex[]generic)(T
hreeStateDB *tdb,DataEntry
[110]
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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) 

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

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

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

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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 <2020-02-02> patch level 5
L3 programming layer <2020-07-17>
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          Entering LaTeX 2.09 COMPATIBILITY MODE
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 This mode attempts to provide an emulation of the LaTeX 2.09
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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
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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]
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[]   \OT1/cmtt/m/n/10 * or WISEPERSONALDIR if it is not present in the current 
directory.[] 

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

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

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[]   \OT1/cmtt/m/n/10 * If the sequences are small enough then it should use ex
plicit memory.[] 
[13]
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[]  \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp
,-gap,-ext,NULL);[] 

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

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

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[]   \OT1/cmtt/m/n/10 * If the sequences are small enough then it should use ex
plicit memory.[] 

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[]  \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp
,-gap,-ext,NULL);[] 
[15]
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[]    \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query
->name,target->name);[] 

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

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

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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[] 

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[]\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[] 

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[]\OT1/cmtt/m/n/10 ROA1_HUMAN           HDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASAS----
-SSQRGRSGS[] 

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[]\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[] 

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[]\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))"[] 

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[]          \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

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[]\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]
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[]    \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)[] 

Overfull \hbox (27.74675pt too wide) in paragraph at lines 1335--1335
[]   \OT1/cmtt/m/n/10 * We could build up something much better, using complexc
onsensi and[] 

Overfull \hbox (43.49661pt too wide) in paragraph at lines 1335--1335
[]   \OT1/cmtt/m/n/10 * other machinery, but not for now <grin>. See the genewi
se code if you[] 
[28]
Overfull \hbox (48.74657pt too wide) in paragraph at lines 1335--1335
[]    \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s
",query->name);[] 

Overfull \hbox (53.99652pt too wide) in paragraph at lines 1335--1335
[]    \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s
",target->name);[] 

Overfull \hbox (27.74675pt too wide) in paragraph at lines 1335--1335
[]   \OT1/cmtt/m/n/10 * cDNA2Gen has alot more parameter space than the paramet
ers to this[] 

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[]   \OT1/cmtt/m/n/10 * program. Firstly we are treating errors similarly on ea
ch side of the[] 

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[]   \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[] 

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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[] 

Overfull \hbox (53.99652pt too wide) in paragraph at lines 1379--1379
[]   \OT1/cmtt/m/n/10 * Really our genomic model should be alot more complex. T
he 'default' one[] 

Overfull \hbox (38.24666pt too wide) in paragraph at lines 1379--1379
[]   \OT1/cmtt/m/n/10 * has 0 at GT----AG for 5' and 3' splice sites, and NEGI 
(= -infinity)[] 

Overfull \hbox (27.74675pt too wide) in paragraph at lines 1379--1379
[]   \OT1/cmtt/m/n/10 * We could build up something much better, using complexc
onsensi and[] 

Overfull \hbox (43.49661pt too wide) in paragraph at lines 1379--1379
[]   \OT1/cmtt/m/n/10 * other machinery, but not for now <grin>. See the genewi
se code if you[] 

Overfull \hbox (48.74657pt too wide) in paragraph at lines 1379--1379
[]    \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s
",query->name);[] 

Overfull \hbox (53.99652pt too wide) in paragraph at lines 1379--1379
[]    \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s
",target->name);[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]\OT1/cmtt/m/n/10 HSHNCPA1        1    GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA
GATGGT-TAT[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]                     \OT1/cmtt/m/n/10 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA
GAT  T T T[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]\OT1/cmtt/m/n/10 HSHNRNPA        2132 GGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGA
GAT--TAT-T[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]\OT1/cmtt/m/n/10 HSHNCPA1        49   TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA
CTGACCGAGG[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]                     \OT1/cmtt/m/n/10 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA
CTGACCGAGG[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]\OT1/cmtt/m/n/10 HSHNRNPA        2178 TTGAACAGTATGGAAAAATTGAAGTGATTGAAATCATGA
CTGACCGAGG[] 
[31]
Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]\OT1/cmtt/m/n/10 HSHNCPA1        98   CAGTGGCAAGAAAAGGGGCTTTGCCT-TAGTAACCTTTG
ACGACCATGA[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]                     \OT1/cmtt/m/n/10 CAGTGGCAAGAAAAGGGGCTTTGCCT T GTAACCTTTG
ACGACCATGA[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]\OT1/cmtt/m/n/10 HSHNRNPA        2227 CAGTGGCAAGAAAAGGGGCTTTGCCTTT-GTAACCTTTG
ACGACCATGA[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]\OT1/cmtt/m/n/10 HSHNCPA1        146  CTCCGTGGATAAGATTGTCA             TTCAGA
AATACCATAC[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]                     \OT1/cmtt/m/n/10 CTCCGTGGATAAGATTGTCA             TTCAGA
AATACCATAC[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]\OT1/cmtt/m/n/10 HSHNRNPA        2275 CTCCGTGGATAAGATTGTCA<-2295:2387->TTCAGA
AATACCATAC[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]\OT1/cmtt/m/n/10 HSHNCPA1        182  TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC
AAAGCAAGAG[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]                     \OT1/cmtt/m/n/10 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC
AAAGCAAGAG[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]\OT1/cmtt/m/n/10 HSHNRNPA        2404 TGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTC
AAAGCAAGAG[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]\OT1/cmtt/m/n/10 HSHNCPA1        231  ATGGCTAGTGCTTCATCCAGCCAAAGAG           
  GTCGAAGT[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]                     \OT1/cmtt/m/n/10 ATGGCTAGTGCTTCATCCAGCCAAAGAG           
  GTCGAAGT[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]\OT1/cmtt/m/n/10 HSHNRNPA        2453 ATGGCTAGTGCTTCATCCAGCCAAAGAG<-2481:2566
->GTCGAAGT[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]\OT1/cmtt/m/n/10 HSHNCPA1        267  GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC
GGTGGGAATG[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]                     \OT1/cmtt/m/n/10 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC
GGTGGGAATG[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]\OT1/cmtt/m/n/10 HSHNRNPA        2575 GGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTC
GGTGGGAATG[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]\OT1/cmtt/m/n/10 HSHNRNPA        2624 ACAACTTCGGTCGTGGAGGAAACTTCAGTGGTCGTG<-2
660:2793->[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]\OT1/cmtt/m/n/10 HSHNCPA1        352  GTNG-CTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT
GGCAGTGGGG[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]                     \OT1/cmtt/m/n/10 GT G CTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT
GGCAGTGGGG[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]\OT1/cmtt/m/n/10 HSHNRNPA        2794 GT-GGCTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGT
GGCAGTGGGG[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]\OT1/cmtt/m/n/10 HSHNCPA1        400  ATGGCTATAATGGATTTGGCAATGATG            
 GAAGCAATT[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]                     \OT1/cmtt/m/n/10 ATGGCTATAATGGATTTGGCAATGATG            
 GAAGCAATT[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]\OT1/cmtt/m/n/10 HSHNRNPA        2842 ATGGCTATAATGGATTTGGCAATGATG<-2869:3805-
>GAAGCAATT[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]\OT1/cmtt/m/n/10 HSHNCPA1        436  TTGGAGGTGGTGGAAGCTACAATGATTTTGGG--tttat
gcA-CAATCA[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]                     \OT1/cmtt/m/n/10 TTGGAGGTGGTGGAAGCTACAATGATTTTGGG  ++ + 
 +A CAATCA[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]\OT1/cmtt/m/n/10 HSHNRNPA        3815 TTGGAGGTGGTGGAAGCTACAATGATTTTGGGAATT-A-
-CAACAATCA[] 
[32]
Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]\OT1/cmtt/m/n/10 HSHNCPA1        482  GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG
AGGCAGAAGC[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]                     \OT1/cmtt/m/n/10 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG
AGGCAGAAGC[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]\OT1/cmtt/m/n/10 HSHNRNPA        3861 GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG
AGGCAGAAGC[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]\OT1/cmtt/m/n/10 HSHNCPA1        531  TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA
CCACGAAACC[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]                     \OT1/cmtt/m/n/10 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA
CCACGAAACC[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]\OT1/cmtt/m/n/10 HSHNRNPA        3910 TCTGGCCCCTATGGCGGTGGAGGCCAATACTTTGCAAAA
CCACGAAACC[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]\OT1/cmtt/m/n/10 HSHNCPA1        580  AAG             GTGGCTATGGCGGTTCCAGCAGC
AGCAGTAGCT[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]                     \OT1/cmtt/m/n/10 AAG             GTGGCTATGGCGGTTCCAGCAGC
AGCAGTAGCT[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]\OT1/cmtt/m/n/10 HSHNRNPA        3959 AAG<-3962:4251->GTGGCTATGGCGGTTCCAGCAGC
AGCAGTAGCT[] 
[33]
Overfull \hbox (22.4968pt too wide) in paragraph at lines 1572--1572
[]\OT1/cmtt/m/n/10 query  type="MySequence*"  name="query" field:len="length_of
_sequence"[] 

Overfull \hbox (27.74675pt too wide) in paragraph at lines 1572--1572
[]\OT1/cmtt/m/n/10 target type="MySequence*"  name="target" field:len="length_o
f_sequence"[] 
[34] [35]
Overfull \hbox (22.4968pt too wide) in paragraph at lines 1600--1600
[]\OT1/cmtt/m/n/10 query  type="MySequence*"  name="query" field:len="length_of
_sequence"[] 

Overfull \hbox (17.24684pt too wide) in paragraph at lines 1634--1634
[] \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_MyProteinSW(seqone,seqtwo,mat,-12,
-2,NULL);[] 

Overfull \hbox (127.49588pt too wide) in paragraph at lines 1634--1634
[]      \OT1/cmtt/m/n/10 fprintf(stdout,"%d,%d are matched with score %d\n",uni
t->i+1,unit->j+1,unit->score);[] 
[36]
Overfull \hbox (22.4968pt too wide) in paragraph at lines 1727--1727
[]\OT1/cmtt/m/n/10 query  type="MySequence*"  name="query" field:len="length_of
_sequence"[] 

Overfull \hbox (27.74675pt too wide) in paragraph at lines 1727--1727
[]\OT1/cmtt/m/n/10 target type="MySequence*"  name="target" field:len="length_o
f_sequence"[] 
[37] [38]
Overfull \hbox (22.4968pt too wide) in paragraph at lines 1849--1849
[]\OT1/cmtt/m/n/10 query  type="MySequence*"  name="query" field:len="length_of
_sequence"[] 

Overfull \hbox (27.74675pt too wide) in paragraph at lines 1849--1849
[]\OT1/cmtt/m/n/10 target type="MySequence*"  name="target" field:len="length_o
f_sequence"[] 
[39]
Overfull \hbox (258.74474pt too wide) in paragraph at lines 1849--1849
[]  \OT1/cmtt/m/n/10 calc="ALPHA_SEQ_SCORE(query,i) + ALPHA_SEQ_SCORE(target,j)
 + mat_alpha.comp[SEQ_POS(query,i)][SEQ_POS(target,j)]"[] 
[40] [41]
Overfull \hbox (20.54509pt too wide) in paragraph at lines 1911--1912
[]\OT1/cmr/m/n/10 The macro Dna-Ma-trix[]Score which is de-fined at the top of 
the cdna2genomic.dy

Overfull \hbox (17.24684pt too wide) in paragraph at lines 1928--1928
[]  \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,i),GENOMIC_CODON(ta
rget,j))"[] 
[42]
Overfull \hbox (53.99652pt too wide) in paragraph at lines 1944--1944
[]        \OT1/cmtt/m/n/10 Mis-type in argument 3 of DNA\_MAT\_SCORE: wanted [b
ase] got [codon][] 

Overfull \hbox (11.99689pt too wide) in paragraph at lines 1955--1955
[]  \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,j),GENOMIC_BASE(tar
get,j))"[] 

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

Overfull \hbox (11.99689pt too wide) in paragraph at lines 1967--1967
[]\OT1/cmtt/m/n/10 expect to paired directly in a function. This is just a warn
ing that[] 
[43]
Overfull \hbox (17.24684pt too wide) in paragraph at lines 2014--2014
[]  \OT1/cmtt/m/n/10 throw_warning("Letter %c does not exist in comparison matr
ix",one);[] 

Overfull \hbox (17.24684pt too wide) in paragraph at lines 2014--2014
[]  \OT1/cmtt/m/n/10 throw_warning("Letter %c does not exist in comparison matr
ix",two);[] 
[44] [45]
Overfull \hbox (74.99634pt too wide) in paragraph at lines 2255--2255
[]  \OT1/cmtt/m/n/10 fprintf(stdout,"dbsearch [options] <protein-seq> <protein-
fasta-database>\n");[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 2255--2255
[]  \OT1/cmtt/m/n/10 /** add more options here sometime, eg comp matrix and gap
 penalty*/[] 

Overfull \hbox (59.24648pt too wide) in paragraph at lines 2255--2255
[]  \OT1/cmtt/m/n/10 /** print out dbsearch options. We don't know here what im
plementations are[] 

Overfull \hbox (74.99634pt too wide) in paragraph at lines 2255--2255
[]      \OT1/cmtt/m/n/10 either possible or how they are specified. Of course, 
there is the problem[] 

Overfull \hbox (59.24648pt too wide) in paragraph at lines 2255--2255
[]      \OT1/cmtt/m/n/10 that we could clash our options with the dbsearchimpl 
options, but that[] 

Overfull \hbox (53.99652pt too wide) in paragraph at lines 2255--2255
[]      \OT1/cmtt/m/n/10 is not too likely, and this makes this program future 
proof wrt to new[] 
[46]
Overfull \hbox (43.49661pt too wide) in paragraph at lines 2255--2255
[]   \OT1/cmtt/m/n/10 * care about which implementation is used, and does not k
now either (!)[] 
[47]
Overfull \hbox (106.49606pt too wide) in paragraph at lines 2255--2255
[]  \OT1/cmtt/m/n/10 /* 10 means a score cutoff of 10, -1 means don't report on
 stderr search progress */[] 

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

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

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

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

Overfull \hbox (1.49698pt too wide) in paragraph at lines 2255--2255
[]      \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta
rget);[] 
[48]
Overfull \hbox (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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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 <2020-02-02> patch level 5
L3 programming layer <2020-07-17>
(/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.
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(/usr/share/texlive/texmf-dist/tex/latex/base/tracefnt.sty)
(/usr/share/texlive/texmf-dist/tex/latex/base/latexsym.sty))
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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[] 

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

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[]      \OT1/cmtt/m/n/10 that we could clash our options with the dbsearchimpl 
options, but that[] 

Overfull \hbox (53.99652pt too wide) in paragraph at lines 2255--2255
[]      \OT1/cmtt/m/n/10 is not too likely, and this makes this program future 
proof wrt to new[] 
[48]
Overfull \hbox (43.49661pt too wide) in paragraph at lines 2255--2255
[]   \OT1/cmtt/m/n/10 * care about which implementation is used, and does not k
now either (!)[] 
[49]
Overfull \hbox (106.49606pt too wide) in paragraph at lines 2255--2255
[]  \OT1/cmtt/m/n/10 /* 10 means a score cutoff of 10, -1 means don't report on
 stderr search progress */[] 

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

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);[] 

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[]      \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,
mat,-12,-2,NULL);[] 

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[]\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);[] 

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[]  \OT1/cmtt/m/n/10 if( search_ProteinSW(dbsi,out,querydb,prodb,mat,-12,-2) !=
 SEARCH_OK )[] 

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[]    \OT1/cmtt/m/n/10 fatal("Some sort of error in the database search. Dieing
 ungracefully");[] 
[51]
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[]      \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta
rget);[] 
[52] [53] [54] [55] [56]
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\OT1/cmr/m/n/10 de-scribed by a "state...endstate" multi-line block. Within eac
h "state...endstate"
[57] [58] [59] [60] [61]
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\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''

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[]        \OT1/cmtt/m/n/10 In matrix ProteinSW - State MATCH asks for source MA
TCH2 but there is[] 

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[]        \OT1/cmtt/m/n/10 Failing simple cross-checks, aborting before calc-li
ne parsing[] 
[62] [63] [64] (./dynamite.aux)

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

 )
(see the transcript file for additional information) </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 dynamite.pdf (64 pages, 217942 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 <2020-02-02> patch level 5
L3 programming layer <2020-07-17>
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2019/12/20 v1.4l Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))
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(/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)))
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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]

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.


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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]

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[9]

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6.

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5.


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.


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[12]

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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]

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[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]

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

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

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[35] [36]

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[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, 206285 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 <2020-02-02> patch level 5
L3 programming layer <2020-07-17>
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2019/12/20 v1.4l 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-pdfmode.def)
(./wise2.aux)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./wise2.toc [2])
[3] [4] [5]
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[]\OT1/cmtt/m/n/10 This program is freely distributed under a GPL. See source d
irectory[] 

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

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

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

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

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

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

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

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

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

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[]                     \OT1/cmtt/m/n/10 RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIE
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]

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 708.

[19] [20] [21] [22]
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[]\OT1/cmr/m/n/10 Algorithms are named in two parts, \OT1/cmr/m/it/10 descripti
ve-word state-number:transition-
[23] [24] [25] [26]
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[]\OT1/cmr/m/n/10 The half-wise pro-tein database, found at ftp://ftp.sanger.ac
.uk/pub/birney/wise2/halfwise 
[27] [28] [29]
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 []\OT1/cmtt/m/n/10 pexon <start-in-dna> <end-in-dna> <start-in-protein> <end-i
n-protein>[] 

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

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 []\OT1/cmtt/m/n/10 230.57 roa1_drome     26  347 HSHNRNPA     1386 3963    0  
  6[] 
[31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] (./wise2.aux)

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 )
(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, 208586 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_testroot -a
   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/aarch64-linux-gnu
	dwz -mdebian/wise/usr/lib/debug/.dwz/aarch64-linux-gnu/wise.debug -M/usr/lib/debug/.dwz/aarch64-linux-gnu/wise.debug -- debian/wise/usr/bin/dba debian/wise/usr/bin/dnal debian/wise/usr/bin/estwise debian/wise/usr/bin/estwisedb debian/wise/usr/bin/genewise debian/wise/usr/bin/genewisedb debian/wise/usr/bin/genomewise debian/wise/usr/bin/promoterwise debian/wise/usr/bin/psw debian/wise/usr/bin/pswdb debian/wise/usr/bin/scanwise debian/wise/usr/bin/scanwise_server
	aarch64-linux-gnu-objcopy --compress-debug-sections debian/wise/usr/lib/debug/.dwz/aarch64-linux-gnu/wise.debug
   dh_strip -a
	install -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/92
	aarch64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/scanwise_server debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/92/3fe901da930d6bed112532778e909185a8894d.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/92/3fe901da930d6bed112532778e909185a8894d.debug
	aarch64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/scanwise_server
	aarch64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/92/3fe901da930d6bed112532778e909185a8894d.debug debian/wise/usr/bin/scanwise_server
	install -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/08
	aarch64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/scanwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/08/589f4b7016f4a1dfa2fcbbe8b8aa9fe5bdb02a.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/08/589f4b7016f4a1dfa2fcbbe8b8aa9fe5bdb02a.debug
	aarch64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/scanwise
	aarch64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/08/589f4b7016f4a1dfa2fcbbe8b8aa9fe5bdb02a.debug debian/wise/usr/bin/scanwise
	install -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/d2
	aarch64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/pswdb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/d2/112286261a563d2161d6f7daf0969102e88ed1.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/d2/112286261a563d2161d6f7daf0969102e88ed1.debug
	aarch64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/pswdb
	aarch64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/d2/112286261a563d2161d6f7daf0969102e88ed1.debug debian/wise/usr/bin/pswdb
	install -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/51
	aarch64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/psw debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/51/79ed0d0d101c95568405c6b47019cbbf0446dc.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/51/79ed0d0d101c95568405c6b47019cbbf0446dc.debug
	aarch64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/psw
	aarch64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/51/79ed0d0d101c95568405c6b47019cbbf0446dc.debug debian/wise/usr/bin/psw
	install -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e5
	aarch64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/promoterwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e5/0f75894414c3f12232e2b8ead996ddeb5ddd98.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e5/0f75894414c3f12232e2b8ead996ddeb5ddd98.debug
	aarch64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/promoterwise
	aarch64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e5/0f75894414c3f12232e2b8ead996ddeb5ddd98.debug debian/wise/usr/bin/promoterwise
	install -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/5d
	aarch64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genomewise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/5d/793d497eb4d93f3f92ad0cc566ae5df534171e.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/5d/793d497eb4d93f3f92ad0cc566ae5df534171e.debug
	aarch64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genomewise
	aarch64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/5d/793d497eb4d93f3f92ad0cc566ae5df534171e.debug debian/wise/usr/bin/genomewise
	install -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/36
	aarch64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genewisedb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/36/6dc46d4581fc20c9fc16aa30c76ff9a172f75b.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/36/6dc46d4581fc20c9fc16aa30c76ff9a172f75b.debug
	aarch64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genewisedb
	aarch64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/36/6dc46d4581fc20c9fc16aa30c76ff9a172f75b.debug debian/wise/usr/bin/genewisedb
	install -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/25
	aarch64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genewise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/25/056330a340e89408c7af35941462596507465c.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/25/056330a340e89408c7af35941462596507465c.debug
	aarch64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genewise
	aarch64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/25/056330a340e89408c7af35941462596507465c.debug debian/wise/usr/bin/genewise
	install -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a9
	aarch64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/estwisedb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a9/c56a1785bd2dc414521cd9192bb96b1256b8da.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a9/c56a1785bd2dc414521cd9192bb96b1256b8da.debug
	aarch64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/estwisedb
	aarch64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a9/c56a1785bd2dc414521cd9192bb96b1256b8da.debug debian/wise/usr/bin/estwisedb
	install -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/21
	aarch64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/estwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/21/98a1f6357350f304e6d94ce764a274cd9a15a1.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/21/98a1f6357350f304e6d94ce764a274cd9a15a1.debug
	aarch64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/estwise
	aarch64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/21/98a1f6357350f304e6d94ce764a274cd9a15a1.debug debian/wise/usr/bin/estwise
	install -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/ed
	aarch64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/dnal debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/ed/90fc054ebc7be375eb4c45a9367b104c32986b.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/ed/90fc054ebc7be375eb4c45a9367b104c32986b.debug
	aarch64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/dnal
	aarch64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/ed/90fc054ebc7be375eb4c45a9367b104c32986b.debug debian/wise/usr/bin/dnal
	aarch64-linux-gnu-objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/dba debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a9/7abd7fd0ad762dc40109f7eb0f666daded7bdc.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a9/7abd7fd0ad762dc40109f7eb0f666daded7bdc.debug
	aarch64-linux-gnu-strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/dba
	aarch64-linux-gnu-objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/a9/7abd7fd0ad762dc40109f7eb0f666daded7bdc.debug debian/wise/usr/bin/dba
	install -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.dwz
	cp --reflink=auto -a debian/wise/usr/lib/debug/.dwz/aarch64-linux-gnu debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.dwz
	rm -fr debian/wise/usr/lib/debug/.dwz
	rmdir -p --ignore-fail-on-non-empty debian/wise/usr/lib/debug
	install -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/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
   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 -DPackage=wise-dbgsym "-DDepends=wise (= \${binary:Version})" "-DDescription=debug symbols for wise" "-DBuild-Ids=08589f4b7016f4a1dfa2fcbbe8b8aa9fe5bdb02a 2198a1f6357350f304e6d94ce764a274cd9a15a1 25056330a340e89408c7af35941462596507465c 366dc46d4581fc20c9fc16aa30c76ff9a172f75b 5179ed0d0d101c95568405c6b47019cbbf0446dc 5d793d497eb4d93f3f92ad0cc566ae5df534171e 923fe901da930d6bed112532778e909185a8894d a97abd7fd0ad762dc40109f7eb0f666daded7bdc a9c56a1785bd2dc414521cd9192bb96b1256b8da d2112286261a563d2161d6f7daf0969102e88ed1 e50f75894414c3f12232e2b8ead996ddeb5ddd98 ed90fc054ebc7be375eb4c45a9367b104c32986b" -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_arm64.deb'.
	dpkg-deb --root-owner-group --build debian/.debhelper/wise/dbgsym-root ..
dpkg-deb: building package 'wise-dbgsym' in '../wise-dbgsym_2.4.1-23_arm64.deb'.
 dpkg-genbuildinfo --build=any
 dpkg-genchanges --build=any >../wise_2.4.1-23_arm64.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2020-09-24T16:01:40Z

Finished
--------

I: Built successfully

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


wise_2.4.1-23_arm64.changes:
----------------------------

Format: 1.8
Date: Sat, 18 Apr 2020 17:57:01 +0200
Source: wise
Binary: wise wise-dbgsym
Built-For-Profiles: cross nocheck
Architecture: arm64
Version: 2.4.1-23
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <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
Checksums-Sha1:
 1f34139f53ad45ccffd678151fc776549e328f50 7799880 wise-dbgsym_2.4.1-23_arm64.deb
 276658c8f43403e885b37d90896ecd7fca2af411 8505 wise_2.4.1-23_arm64.buildinfo
 4d0f656413ca362f40c54c17f66c6f32709ccdfc 990636 wise_2.4.1-23_arm64.deb
Checksums-Sha256:
 a0c5aa4734ce12400d4e657e615396112485eb5538c6fd461920a113394e23f0 7799880 wise-dbgsym_2.4.1-23_arm64.deb
 b8046fb3b174f59dd917a2ce41f3eff8413ebfdbefa7e6a0fa5ec7bb3f80d795 8505 wise_2.4.1-23_arm64.buildinfo
 26f3012ad256a2a83013a032e1795e62070f3b8ca19e86057920d4ec3bf8ae10 990636 wise_2.4.1-23_arm64.deb
Files:
 7f17ac933c3c9b84b7ef6f99746402de 7799880 debug optional wise-dbgsym_2.4.1-23_arm64.deb
 f744adc5b7ed534e56d758c6aca364e0 8505 science optional wise_2.4.1-23_arm64.buildinfo
 f2cc1e54ea90639d03395edde5f683f9 990636 science optional wise_2.4.1-23_arm64.deb

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

Format: 1.0
Source: wise
Binary: wise wise-dbgsym
Architecture: arm64
Version: 2.4.1-23
Checksums-Md5:
 7f17ac933c3c9b84b7ef6f99746402de 7799880 wise-dbgsym_2.4.1-23_arm64.deb
 f2cc1e54ea90639d03395edde5f683f9 990636 wise_2.4.1-23_arm64.deb
Checksums-Sha1:
 1f34139f53ad45ccffd678151fc776549e328f50 7799880 wise-dbgsym_2.4.1-23_arm64.deb
 4d0f656413ca362f40c54c17f66c6f32709ccdfc 990636 wise_2.4.1-23_arm64.deb
Checksums-Sha256:
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 26f3012ad256a2a83013a032e1795e62070f3b8ca19e86057920d4ec3bf8ae10 990636 wise_2.4.1-23_arm64.deb
Build-Origin: Debian
Build-Architecture: amd64
Build-Date: Thu, 24 Sep 2020 16:01:40 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
 autoconf (= 2.69-11.1),
 automake (= 1:1.16.2-4),
 autopoint (= 0.19.8.1-10),
 autotools-dev (= 20180224.1),
 base-files (= 11),
 base-passwd (= 3.5.47),
 bash (= 5.0-7),
 binutils (= 2.35.1-1),
 binutils-common (= 2.35.1-1),
 binutils-x86-64-linux-gnu (= 2.35.1-1),
 bsdextrautils (= 2.36-3+b1),
 bsdutils (= 1:2.36-3+b1),
 build-essential (= 12.8),
 bzip2 (= 1.0.8-4),
 coreutils (= 8.32-4+b1),
 cpp (= 4:10.2.0-1),
 cpp-10 (= 10.2.0-9),
 dash (= 0.5.10.2-7),
 debconf (= 1.5.74),
 debhelper (= 13.2.1),
 debianutils (= 4.11.1),
 dh-autoreconf (= 19),
 dh-strip-nondeterminism (= 1.9.0-1),
 diffutils (= 1:3.7-3),
 docbook (= 4.5-6),
 docbook-to-man (= 1:2.0.0-45),
 dpkg (= 1.20.5),
 dpkg-dev (= 1.20.5),
 dwz (= 0.13-5),
 file (= 1:5.38-5),
 findutils (= 4.7.0-1),
 fontconfig-config (= 2.13.1-4.2),
 fonts-dejavu-core (= 2.37-2),
 fonts-lmodern (= 2.004.5-6),
 fonts-urw-base35 (= 20200910-1),
 g++ (= 4:10.2.0-1),
 g++-10 (= 10.2.0-9),
 gcc (= 4:10.2.0-1),
 gcc-10 (= 10.2.0-9),
 gcc-10-base (= 10.2.0-9),
 gettext (= 0.19.8.1-10),
 gettext-base (= 0.19.8.1-10),
 ghostscript (= 9.53.1~dfsg-2),
 grep (= 3.4-1),
 groff-base (= 1.22.4-5),
 gzip (= 1.10-2),
 hevea (= 2.34-2),
 hostname (= 3.23),
 init-system-helpers (= 1.58),
 intltool-debian (= 0.35.0+20060710.5),
 libacl1 (= 2.2.53-8),
 libarchive-zip-perl (= 1.68-1),
 libasan6 (= 10.2.0-9),
 libatomic1 (= 10.2.0-9),
 libattr1 (= 1:2.4.48-5),
 libaudit-common (= 1:2.8.5-3),
 libaudit1 (= 1:2.8.5-3+b1),
 libavahi-client3 (= 0.8-3),
 libavahi-common-data (= 0.8-3),
 libavahi-common3 (= 0.8-3),
 libbinutils (= 2.35.1-1),
 libblkid-dev (= 2.36-3+b1),
 libblkid1 (= 2.36-3+b1),
 libbrotli1 (= 1.0.9-2),
 libbsd0 (= 0.10.0-1),
 libbz2-1.0 (= 1.0.8-4),
 libc-bin (= 2.31-3),
 libc-dev-bin (= 2.31-3),
 libc6 (= 2.31-3),
 libc6-dev (= 2.31-3),
 libcairo2 (= 1.16.0-4),
 libcap-ng0 (= 0.7.9-2.2),
 libcc1-0 (= 10.2.0-9),
 libcom-err2 (= 1.45.6-1),
 libcroco3 (= 0.6.13-1),
 libcrypt-dev (= 1:4.4.17-1),
 libcrypt1 (= 1:4.4.17-1),
 libctf-nobfd0 (= 2.35.1-1),
 libctf0 (= 2.35.1-1),
 libcups2 (= 2.3.3-3),
 libdatrie1 (= 0.2.12-3),
 libdb5.3 (= 5.3.28+dfsg1-0.6),
 libdbus-1-3 (= 1.12.20-1),
 libdebconfclient0 (= 0.254),
 libdebhelper-perl (= 13.2.1),
 libdpkg-perl (= 1.20.5),
 libelf1 (= 0.181-1),
 libexpat1 (= 2.2.9-1),
 libffi-dev (= 3.3-4),
 libffi7 (= 3.3-4),
 libfile-stripnondeterminism-perl (= 1.9.0-1),
 libfontconfig1 (= 2.13.1-4.2),
 libfontenc1 (= 1:1.1.4-1),
 libfreetype6 (= 2.10.2+dfsg-3),
 libgcc-10-dev (= 10.2.0-9),
 libgcc-s1 (= 10.2.0-9),
 libgcrypt20 (= 1.8.6-2),
 libgdbm-compat4 (= 1.18.1-5.1),
 libgdbm6 (= 1.18.1-5.1),
 libglib2.0-0 (= 2.66.0-2),
 libglib2.0-bin (= 2.66.0-2),
 libglib2.0-data (= 2.66.0-2),
 libglib2.0-dev (= 2.66.0-2),
 libglib2.0-dev-bin (= 2.66.0-2),
 libgmp10 (= 2:6.2.0+dfsg-6),
 libgnutls30 (= 3.6.15-4),
 libgomp1 (= 10.2.0-9),
 libgpg-error0 (= 1.38-2),
 libgraphite2-3 (= 1.3.14-1),
 libgs9 (= 9.53.1~dfsg-2),
 libgs9-common (= 9.53.1~dfsg-2),
 libgssapi-krb5-2 (= 1.17-10),
 libharfbuzz0b (= 2.6.7-1),
 libhogweed6 (= 3.6-2),
 libice6 (= 2:1.0.10-1),
 libicu67 (= 67.1-4),
 libidn11 (= 1.33-2.4),
 libidn2-0 (= 2.3.0-1),
 libijs-0.35 (= 0.35-15),
 libisl22 (= 0.22.1-1),
 libitm1 (= 10.2.0-9),
 libjbig0 (= 2.1-3.1+b2),
 libjbig2dec0 (= 0.19-1),
 libjpeg62-turbo (= 1:2.0.5-1.1),
 libjs-jquery (= 3.5.1+dfsg-4),
 libk5crypto3 (= 1.17-10),
 libkeyutils1 (= 1.6.1-2),
 libkpathsea6 (= 2020.20200327.54578-5),
 libkrb5-3 (= 1.17-10),
 libkrb5support0 (= 1.17-10),
 liblcms2-2 (= 2.9-4+b1),
 liblsan0 (= 10.2.0-9),
 liblz4-1 (= 1.9.2-2),
 liblzma5 (= 5.2.4-1+b1),
 libmagic-mgc (= 1:5.38-5),
 libmagic1 (= 1:5.38-5),
 libmime-charset-perl (= 1.012.2-1),
 libmount-dev (= 2.36-3+b1),
 libmount1 (= 2.36-3+b1),
 libmpc3 (= 1.2.0-1),
 libmpfr6 (= 4.1.0-3),
 libncursesw6 (= 6.2+20200918-1),
 libnetpbm10 (= 2:10.0-15.3+b2),
 libnettle8 (= 3.6-2),
 libopenjp2-7 (= 2.3.1-1),
 libosp5 (= 1.5.2-13+b1),
 libp11-kit0 (= 0.23.21-2),
 libpam-modules (= 1.3.1-5),
 libpam-modules-bin (= 1.3.1-5),
 libpam-runtime (= 1.3.1-5),
 libpam0g (= 1.3.1-5),
 libpaper-utils (= 1.1.28+b1),
 libpaper1 (= 1.1.28+b1),
 libpcre16-3 (= 2:8.39-13),
 libpcre2-16-0 (= 10.34-7),
 libpcre2-32-0 (= 10.34-7),
 libpcre2-8-0 (= 10.34-7),
 libpcre2-dev (= 10.34-7),
 libpcre2-posix2 (= 10.34-7),
 libpcre3 (= 2:8.39-13),
 libpcre3-dev (= 2:8.39-13),
 libpcre32-3 (= 2:8.39-13),
 libpcrecpp0v5 (= 2:8.39-13),
 libperl5.30 (= 5.30.3-4),
 libpipeline1 (= 1.5.3-1),
 libpixman-1-0 (= 0.36.0-1),
 libpng16-16 (= 1.6.37-3),
 libptexenc1 (= 2020.20200327.54578-5),
 libpython3-stdlib (= 3.8.2-3),
 libpython3.8-minimal (= 3.8.6~rc1-2),
 libpython3.8-stdlib (= 3.8.6~rc1-2),
 libquadmath0 (= 10.2.0-9),
 libreadline8 (= 8.0-4),
 libseccomp2 (= 2.4.4-1),
 libselinux1 (= 3.1-2),
 libselinux1-dev (= 3.1-2),
 libsepol1 (= 3.1-1),
 libsepol1-dev (= 3.1-1),
 libsigsegv2 (= 2.12-2),
 libsm6 (= 2:1.2.3-1),
 libsmartcols1 (= 2.36-3+b1),
 libsombok3 (= 2.4.0-2+b1),
 libsqlite3-0 (= 3.33.0-1),
 libssl1.1 (= 1.1.1g-1),
 libstdc++-10-dev (= 10.2.0-9),
 libstdc++6 (= 10.2.0-9),
 libsub-override-perl (= 0.09-2),
 libsynctex2 (= 2020.20200327.54578-5),
 libsystemd0 (= 246.6-1),
 libtasn1-6 (= 4.16.0-2),
 libteckit0 (= 2.5.10+ds1-3),
 libtexlua53 (= 2020.20200327.54578-5),
 libtexluajit2 (= 2020.20200327.54578-5),
 libthai-data (= 0.1.28-3),
 libthai0 (= 0.1.28-3),
 libtiff5 (= 4.1.0+git191117-2),
 libtinfo6 (= 6.2+20200918-1),
 libtool (= 2.4.6-14),
 libtsan0 (= 10.2.0-9),
 libubsan1 (= 10.2.0-9),
 libuchardet0 (= 0.0.7-1),
 libudev1 (= 246.6-1),
 libunicode-linebreak-perl (= 0.0.20190101-1+b2),
 libunistring2 (= 0.9.10-4),
 libuuid1 (= 2.36-3+b1),
 libwebp6 (= 0.6.1-2+b1),
 libx11-6 (= 2:1.6.12-1),
 libx11-data (= 2:1.6.12-1),
 libxau6 (= 1:1.0.8-1+b2),
 libxaw7 (= 2:1.0.13-1+b2),
 libxcb-render0 (= 1.14-2),
 libxcb-shm0 (= 1.14-2),
 libxcb1 (= 1.14-2),
 libxdmcp6 (= 1:1.1.2-3),
 libxext6 (= 2:1.3.3-1+b2),
 libxi6 (= 2:1.7.10-1),
 libxml2 (= 2.9.10+dfsg-6),
 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 (= 1.4.5+dfsg-4),
 libzzip-0-13 (= 0.13.62-3.2),
 linux-libc-dev (= 5.8.10-1),
 lmodern (= 2.004.5-6),
 login (= 1:4.8.1-1),
 lsb-base (= 11.1.0),
 m4 (= 1.4.18-4),
 make (= 4.3-4),
 man-db (= 2.9.3-2),
 mawk (= 1.3.4.20200120-2),
 mime-support (= 3.64),
 ncurses-base (= 6.2+20200918-1),
 ncurses-bin (= 6.2+20200918-1),
 netpbm (= 2:10.0-15.3+b2),
 node-jquery (= 3.5.1+dfsg-4),
 opensp (= 1.5.2-13+b1),
 patch (= 2.7.6-6),
 perl (= 5.30.3-4),
 perl-base (= 5.30.3-4),
 perl-modules-5.30 (= 5.30.3-4),
 pkg-config (= 0.29.2-1),
 po-debconf (= 1.0.21),
 poppler-data (= 0.4.9-2),
 python3 (= 3.8.2-3),
 python3-distutils (= 3.8.5-1),
 python3-lib2to3 (= 3.8.5-1),
 python3-minimal (= 3.8.2-3),
 python3.8 (= 3.8.6~rc1-2),
 python3.8-minimal (= 3.8.6~rc1-2),
 readline-common (= 8.0-4),
 sed (= 4.7-1),
 sensible-utils (= 0.0.12+nmu1),
 sgml-base (= 1.30),
 sgml-data (= 2.0.11),
 sysvinit-utils (= 2.96-5),
 t1utils (= 1.41-4),
 tar (= 1.30+dfsg-7),
 tex-common (= 6.15),
 texlive-base (= 2020.20200804-3),
 texlive-binaries (= 2020.20200327.54578-5),
 texlive-extra-utils (= 2020.20200804-3),
 texlive-latex-base (= 2020.20200804-3),
 texlive-luatex (= 2020.20200804-3),
 texlive-plain-generic (= 2020.20200804-3),
 ucf (= 3.0043),
 util-linux (= 2.36-3+b1),
 uuid-dev (= 2.36-3+b1),
 x11-common (= 1:7.7+20),
 xdg-utils (= 1.1.3-2),
 xfonts-encodings (= 1:1.0.4-2),
 xfonts-utils (= 1:7.7+6),
 xml-core (= 0.18+nmu1),
 xz-utils (= 5.2.4-1+b1),
 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_US.UTF-8"
 LC_ALL="C.UTF-8"
 SOURCE_DATE_EPOCH="1587225421"


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


wise-dbgsym_2.4.1-23_arm64.deb
------------------------------

 new Debian package, version 2.0.
 size 7799880 bytes: control archive=1136 bytes.
     812 bytes,    12 lines      control              
    1354 bytes,    13 lines      md5sums              
 Package: wise-dbgsym
 Source: wise
 Version: 2.4.1-23
 Auto-Built-Package: debug-symbols
 Architecture: arm64
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 9239
 Depends: wise (= 2.4.1-23)
 Section: debug
 Priority: optional
 Description: debug symbols for wise
 Build-Ids: 08589f4b7016f4a1dfa2fcbbe8b8aa9fe5bdb02a 2198a1f6357350f304e6d94ce764a274cd9a15a1 25056330a340e89408c7af35941462596507465c 366dc46d4581fc20c9fc16aa30c76ff9a172f75b 5179ed0d0d101c95568405c6b47019cbbf0446dc 5d793d497eb4d93f3f92ad0cc566ae5df534171e 923fe901da930d6bed112532778e909185a8894d a97abd7fd0ad762dc40109f7eb0f666daded7bdc a9c56a1785bd2dc414521cd9192bb96b1256b8da d2112286261a563d2161d6f7daf0969102e88ed1 e50f75894414c3f12232e2b8ead996ddeb5ddd98 ed90fc054ebc7be375eb4c45a9367b104c32986b

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/
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-rw-r--r-- root/root    520512 2020-04-18 15:57 ./usr/lib/debug/.build-id/08/589f4b7016f4a1dfa2fcbbe8b8aa9fe5bdb02a.debug
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drwxr-xr-x root/root         0 2020-04-18 15:57 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root         0 2020-04-18 15:57 ./usr/lib/debug/.dwz/aarch64-linux-gnu/
-rw-r--r-- root/root     92080 2020-04-18 15:57 ./usr/lib/debug/.dwz/aarch64-linux-gnu/wise.debug
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drwxr-xr-x root/root         0 2020-04-18 15:57 ./usr/share/doc/
lrwxrwxrwx root/root         0 2020-04-18 15:57 ./usr/share/doc/wise-dbgsym -> wise


wise_2.4.1-23_arm64.deb
-----------------------

 new Debian package, version 2.0.
 size 990636 bytes: control archive=1964 bytes.
    1720 bytes,    33 lines      control              
    1742 bytes,    29 lines      md5sums              
 Package: wise
 Version: 2.4.1-23
 Architecture: arm64
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 9426
 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    313568 2020-04-18 15:57 ./usr/bin/dba
-rwxr-xr-x root/root    219296 2020-04-18 15:57 ./usr/bin/dnal
-rwxr-xr-x root/root   1749224 2020-04-18 15:57 ./usr/bin/estwise
-rwxr-xr-x root/root   1761616 2020-04-18 15:57 ./usr/bin/estwisedb
-rwxr-xr-x root/root   1753416 2020-04-18 15:57 ./usr/bin/genewise
-rwxr-xr-x root/root   1761680 2020-04-18 15:57 ./usr/bin/genewisedb
-rwxr-xr-x root/root    354424 2020-04-18 15:57 ./usr/bin/genomewise
-rwxr-xr-x root/root    383136 2020-04-18 15:57 ./usr/bin/promoterwise
-rwxr-xr-x root/root    317600 2020-04-18 15:57 ./usr/bin/psw
-rwxr-xr-x root/root    325872 2020-04-18 15:57 ./usr/bin/pswdb
-rwxr-xr-x root/root    469152 2020-04-18 15:57 ./usr/bin/scanwise
-rwxr-xr-x root/root    198800 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:amd64
Filtered Build-Depends: lintian:amd64
dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-lintian-dummy.deb'.
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Install lintian build dependencies (apt-based resolver)
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Installing build dependencies
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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
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  libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl
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  libipc-system-simple-perl libiterator-perl libiterator-util-perl
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  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
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  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
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  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
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  liblist-utilsby-perl liblzo2-2 libmarkdown2 libmodule-implementation-perl
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  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:arm64 unzip
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Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libpath-tiny-perl all 0.114-1 [53.6 kB]
Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libperlio-gzip-perl amd64 0.19-1+b6 [17.4 kB]
Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libproc-processtable-perl amd64 0.59-2 [45.7 kB]
Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libsereal-decoder-perl amd64 4.018+ds-1 [98.9 kB]
Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libsereal-encoder-perl amd64 4.018+ds-1 [103 kB]
Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-levenshteinxs-perl amd64 0.03-4+b7 [8696 B]
Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-markdown-discount-perl amd64 0.12-1 [12.7 kB]
Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-xslate-perl amd64 3.5.8-1 [198 kB]
Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libtime-duration-perl all 1.21-1 [13.7 kB]
Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 libtime-moment-perl amd64 0.44-1+b2 [75.1 kB]
Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 libtimedate-perl all 2.3300-1 [39.2 kB]
Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 libtype-tiny-perl all 1.010006-1 [339 kB]
Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 libunicode-utf8-perl amd64 0.62-1+b1 [20.2 kB]
Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 liburi-perl all 1.76-2 [90.2 kB]
Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-0-2 amd64 0.2.2-1 [49.6 kB]
Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-libyaml-perl amd64 0.82+repack-1 [35.6 kB]
Get:81 http://debian.oregonstate.edu/debian unstable/main amd64 lzip amd64 1.21-8 [84.3 kB]
Get:82 http://debian.oregonstate.edu/debian unstable/main amd64 lzop amd64 1.04-1 [83.4 kB]
Get:83 http://debian.oregonstate.edu/debian unstable/main amd64 patchutils amd64 0.4.2-1 [77.5 kB]
Get:84 http://debian.oregonstate.edu/debian unstable/main amd64 unzip amd64 6.0-25 [172 kB]
Get:85 http://debian.oregonstate.edu/debian unstable/main amd64 lintian all 2.95.0 [1272 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libnamespace-clean-perl (0.27-1) ...
Setting up lintian (2.95.0) ...
Setting up sbuild-build-depends-lintian-dummy:arm64 (0.invalid.0) ...
Processing triggers for libc-bin (2.31-3) ...
Processing triggers for man-db (2.9.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Processing triggers for mime-support (3.64) ...

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: amd64
Build Profiles: cross nocheck
Build Type: any
Build-Space: 184380
Build-Time: 162
Distribution: unstable
Foreign Architectures: arm64
Host Architecture: arm64
Install-Time: 62
Job: wise_2.4.1-23
Lintian: pass
Machine Architecture: amd64
Package: wise
Package-Time: 237
Source-Version: 2.4.1-23
Space: 184380
Status: successful
Version: 2.4.1-23
--------------------------------------------------------------------------------
Finished at 2020-09-24T16:01:40Z
Build needed 00:03:57, 184380k disk space