Thu Mar 27 23:59:29 UTC 2025  I: starting to build wise/unstable/amd64 on jenkins on '2025-03-27 23:59'
Thu Mar 27 23:59:29 UTC 2025  I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_8/52279/console.log
Thu Mar 27 23:59:29 UTC 2025  I: Downloading source for unstable/wise=2.4.1-27
--2025-03-27 23:59:29--  http://deb.debian.org/debian/pool/main/w/wise/wise_2.4.1-27.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2166 (2.1K) [text/prs.lines.tag]
Saving to: ‘wise_2.4.1-27.dsc’

     0K ..                                                    100%  395M=0s

2025-03-27 23:59:29 (395 MB/s) - ‘wise_2.4.1-27.dsc’ saved [2166/2166]

Thu Mar 27 23:59:29 UTC 2025  I: wise_2.4.1-27.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 3.0 (quilt)
Source: wise
Binary: wise, wise-doc, wise-data
Architecture: any all
Version: 2.4.1-27
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller@debian.org>, Charles Plessy <plessy@debian.org>, Andreas Tille <tille@debian.org>
Homepage: https://www.ebi.ac.uk/~birney/wise2/
Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/wise
Vcs-Git: https://salsa.debian.org/med-team/wise.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), texlive-latex-base, texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev, libfl-dev
Package-List:
 wise deb science optional arch=any
 wise-data deb doc optional arch=all
 wise-doc deb doc optional arch=all
Checksums-Sha1:
 50215e0541ed043d2ee44463da1b1a0d5272d724 3410178 wise_2.4.1.orig.tar.gz
 d30f85476067817e8d23786088d4c6faf4204242 41828 wise_2.4.1-27.debian.tar.xz
Checksums-Sha256:
 0aec5e30739110783517a429606249fc6c5fd0d65171c1a6d79ecc5ff81d2935 3410178 wise_2.4.1.orig.tar.gz
 39e7538545d33a9d298c1d7be4d83f34aa89eee0b3eeeedd5bdd88559da864d8 41828 wise_2.4.1-27.debian.tar.xz
Files:
 9e90132c19a653831ce63b5af7f08302 3410178 wise_2.4.1.orig.tar.gz
 e50700fd299cde6430358d8d8b89b3bc 41828 wise_2.4.1-27.debian.tar.xz


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Thu Mar 27 23:59:29 UTC 2025  I: Checking whether the package is not for us
Thu Mar 27 23:59:29 UTC 2025  I: Starting 1st build on remote node ionos15-amd64.debian.net.
Thu Mar 27 23:59:29 UTC 2025  I: Preparing to do remote build '1' on ionos15-amd64.debian.net.
Fri Mar 28 00:08:18 UTC 2025  I: Deleting $TMPDIR on ionos15-amd64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Wed Apr 29 18:22:33 -12 2026
I: pbuilder-time-stamp: 1777530153
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [wise_2.4.1-27.dsc]
I: copying [./wise_2.4.1.orig.tar.gz]
I: copying [./wise_2.4.1-27.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./wise_2.4.1-27.dsc: unsupported subcommand
dpkg-source: info: extracting wise in wise-2.4.1
dpkg-source: info: unpacking wise_2.4.1.orig.tar.gz
dpkg-source: info: unpacking wise_2.4.1-27.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying 01_welcome-csh.patch
dpkg-source: info: applying 02_isnumber.patch
dpkg-source: info: applying 03_doc-nodycache.patch
dpkg-source: info: applying 04_wise2-pdflatex-update.patch
dpkg-source: info: applying 05_glib2.patch
dpkg-source: info: applying 06_getline.patch
dpkg-source: info: applying 07_ld--as-needed.patch
dpkg-source: info: applying 08_mayhem.patch
dpkg-source: info: applying 09_dnal-add-return-statement.patch
dpkg-source: info: applying 10_fix_path_to_data_files.patch
dpkg-source: info: applying 11_consistent_manual_dates.patch
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying cross.patch
dpkg-source: info: applying implicit-function-declaration.patch
dpkg-source: info: applying executable-is-script.patch
dpkg-source: info: applying gcc-14.patch
dpkg-source: info: applying fix_blhc.patch
dpkg-source: info: applying fix_ftbfs_with_gcc-15.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/900143/tmp/hooks/D02_print_environment starting
I: set
  BUILDDIR='/build/reproducible-path'
  BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
  BUILDUSERNAME='pbuilder1'
  BUILD_ARCH='amd64'
  DEBIAN_FRONTEND='noninteractive'
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 '
  DISTRIBUTION='unstable'
  HOME='/root'
  HOST_ARCH='amd64'
  IFS=' 	
  '
  INVOCATION_ID='6bd76dc7dc874485859e566720fa52ed'
  LANG='C'
  LANGUAGE='en_US:en'
  LC_ALL='C'
  MAIL='/var/mail/root'
  OPTIND='1'
  PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
  PBCURRENTCOMMANDLINEOPERATION='build'
  PBUILDER_OPERATION='build'
  PBUILDER_PKGDATADIR='/usr/share/pbuilder'
  PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
  PBUILDER_SYSCONFDIR='/etc'
  PPID='900143'
  PS1='# '
  PS2='> '
  PS4='+ '
  PWD='/'
  SHELL='/bin/bash'
  SHLVL='2'
  SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.ahawirbV/pbuilderrc_aELG --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ahawirbV/b1 --logfile b1/build.log wise_2.4.1-27.dsc'
  SUDO_GID='111'
  SUDO_UID='106'
  SUDO_USER='jenkins'
  TERM='unknown'
  TZ='/usr/share/zoneinfo/Etc/GMT+12'
  USER='root'
  _='/usr/bin/systemd-run'
  http_proxy='http://213.165.73.152:3128'
I: uname -a
  Linux ionos15-amd64 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux
I: ls -l /bin
  lrwxrwxrwx 1 root root 7 Mar  4  2025 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/900143/tmp/hooks/D02_print_environment finished
 -> Attempting to satisfy build-dependencies
 -> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
 This package was created automatically by pbuilder to satisfy the
 build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), texlive-latex-base, texlive-extra-utils, hevea, docbook-to-man, libglib2.0-dev, libfl-dev
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19805 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
 pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
  Package debhelper-compat is not installed.
 pbuilder-satisfydepends-dummy depends on texlive-latex-base; however:
  Package texlive-latex-base is not installed.
 pbuilder-satisfydepends-dummy depends on texlive-extra-utils; however:
  Package texlive-extra-utils is not installed.
 pbuilder-satisfydepends-dummy depends on hevea; however:
  Package hevea is not installed.
 pbuilder-satisfydepends-dummy depends on docbook-to-man; however:
  Package docbook-to-man is not installed.
 pbuilder-satisfydepends-dummy depends on libglib2.0-dev; however:
  Package libglib2.0-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libfl-dev; however:
  Package libfl-dev is not installed.

Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
  autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} docbook{a} docbook-to-man{a} dwz{a} file{a} flex{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-lmodern{a} fonts-urw-base35{a} gettext{a} gettext-base{a} ghostscript{a} girepository-tools{a} groff-base{a} hevea{a} hicolor-icon-theme{a} imagemagick{a} imagemagick-7-common{a} imagemagick-7.q16{a} intltool-debian{a} libarchive-zip-perl{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libblkid-dev{a} libbrotli1{a} libcairo2{a} libcom-err2{a} libcups2t64{a} libdatrie1{a} libdav1d7{a} libdbus-1-3{a} libde265-0{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libffi-dev{a} libffi8{a} libfftw3-double3{a} libfile-homedir-perl{a} libfile-stripnondeterminism-perl{a} libfile-which-perl{a} libfl-dev{a} libfl2{a} libfontconfig1{a} libfontenc1{a} libfreetype6{a} libgio-2.0-dev{a} libgio-2.0-dev-bin{a} libgirepository-2.0-0{a} libglib2.0-0t64{a} libglib2.0-bin{a} libglib2.0-data{a} libglib2.0-dev{a} libglib2.0-dev-bin{a} libgnutls30t64{a} libgraphite2-3{a} libgs-common{a} libgs10{a} libgs10-common{a} libgssapi-krb5-2{a} libharfbuzz0b{a} libheif-plugin-dav1d{a} libheif-plugin-libde265{a} libheif1{a} libice6{a} libicu76{a} libidn12{a} libidn2-0{a} libijs-0.35{a} libjbig0{a} libjbig2dec0{a} libjpeg62-turbo{a} libjs-jquery{a} libk5crypto3{a} libkeyutils1{a} libkpathsea6{a} libkrb5-3{a} libkrb5support0{a} liblcms2-2{a} liblerc4{a} liblqr-1-0{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmagickcore-7.q16-10{a} libmagickwand-7.q16-10{a} libmime-charset-perl{a} libmount-dev{a} libmpfi0{a} libnetpbm11t64{a} libopenjp2-7{a} libosp5{a} libp11-kit0{a} libpaper-utils{a} libpaper2{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix3{a} libpipeline1{a} libpixman-1-0{a} libpkgconf3{a} libpng16-16t64{a} libpotrace0{a} libproc2-0{a} libptexenc1{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libraw23t64{a} libreadline8t64{a} libselinux1-dev{a} libsepol-dev{a} libsharpyuv0{a} libsm6{a} libsombok3{a} libsynctex2{a} libsysprof-capture-4-dev{a} libtasn1-6{a} libteckit0{a} libtexlua53-5{a} libtext-charwidth-perl{a} libtext-wrapi18n-perl{a} libthai-data{a} libthai0{a} libtiff6{a} libtool{a} libuchardet0{a} libunicode-linebreak-perl{a} libunistring5{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxi6{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6t64{a} libyaml-tiny-perl{a} libzzip-0-13t64{a} lmodern{a} m4{a} man-db{a} media-types{a} native-architecture{a} netbase{a} netpbm{a} opensp{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} poppler-data{a} procps{a} python3{a} python3-minimal{a} python3-packaging{a} python3.13{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sgml-data{a} t1utils{a} tex-common{a} texlive-base{a} texlive-binaries{a} texlive-extra-utils{a} texlive-latex-base{a} texlive-luatex{a} texlive-plain-generic{a} tzdata{a} ucf{a} uuid-dev{a} x11-common{a} xdg-utils{a} xfonts-encodings{a} xfonts-utils{a} xml-core{a} zlib1g-dev{a} 
The following packages are RECOMMENDED but will NOT be installed:
  ca-certificates curl dbus dvisvgm fonts-droid-fallback javascript-common krb5-locales libarchive-cpio-perl libfile-mimeinfo-perl libheif-plugin-aomenc libheif-plugin-x265 liblog-log4perl-perl libltdl-dev libmagickcore-7.q16-10-extra libmail-sendmail-perl libnet-dbus-perl libx11-protocol-perl linux-sysctl-defaults lynx psmisc ruby shared-mime-info texlive-latex-recommended wget x11-utils x11-xserver-utils xdg-user-dirs 
0 packages upgraded, 200 newly installed, 0 to remove and 0 not upgraded.
Need to get 253 MB of archives. After unpacking 642 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-7 [294 kB]
Get: 2 http://deb.debian.org/debian unstable/main amd64 flex amd64 2.6.4-8.2+b4 [423 kB]
Get: 3 http://deb.debian.org/debian unstable/main amd64 libfftw3-double3 amd64 3.3.10-2+b1 [781 kB]
Get: 4 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.1-1 [108 kB]
Get: 5 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB]
Get: 6 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.47-1.1 [282 kB]
Get: 7 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB]
Get: 8 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB]
Get: 9 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB]
Get: 10 http://deb.debian.org/debian unstable/main amd64 libfontenc1 amd64 1:1.1.8-1+b2 [23.3 kB]
Get: 11 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+24 [217 kB]
Get: 12 http://deb.debian.org/debian unstable/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB]
Get: 13 http://deb.debian.org/debian unstable/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB]
Get: 14 http://deb.debian.org/debian unstable/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB]
Get: 15 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-2.2 [318 kB]
Get: 16 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-2.2 [391 kB]
Get: 17 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.5.0-0.1 [116 kB]
Get: 18 http://deb.debian.org/debian unstable/main amd64 libdav1d7 amd64 1.5.1-1 [559 kB]
Get: 19 http://deb.debian.org/debian unstable/main amd64 libheif-plugin-dav1d amd64 1.19.7-1 [11.7 kB]
Get: 20 http://deb.debian.org/debian unstable/main amd64 libde265-0 amd64 1.0.15-1+b3 [189 kB]
Get: 21 http://deb.debian.org/debian unstable/main amd64 libheif-plugin-libde265 amd64 1.19.7-1 [15.3 kB]
Get: 22 http://deb.debian.org/debian unstable/main amd64 libheif1 amd64 1.19.7-1 [520 kB]
Get: 23 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB]
Get: 24 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3.1 [168 kB]
Get: 25 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB]
Get: 26 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB]
Get: 27 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.84.0-2 [1513 kB]
Get: 28 http://deb.debian.org/debian unstable/main amd64 liblqr-1-0 amd64 0.4.2-2.1+b2 [29.5 kB]
Get: 29 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.5.4-4 [416 kB]
Get: 30 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.3-2 [204 kB]
Get: 31 http://deb.debian.org/debian unstable/main amd64 libraw23t64 amd64 0.21.3-1+b1 [390 kB]
Get: 32 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB]
Get: 33 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB]
Get: 34 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.5.0-0.1 [318 kB]
Get: 35 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.7.0-1 [345 kB]
Get: 36 http://deb.debian.org/debian unstable/main amd64 libwebpdemux2 amd64 1.5.0-0.1 [113 kB]
Get: 37 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.5.0-0.1 [126 kB]
Get: 38 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB]
Get: 39 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB]
Get: 40 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB]
Get: 41 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.12-1 [343 kB]
Get: 42 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB]
Get: 43 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB]
Get: 44 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.4 [698 kB]
Get: 45 http://deb.debian.org/debian unstable/main amd64 imagemagick-7-common all 8:7.1.1.43+dfsg1-1 [67.4 kB]
Get: 46 http://deb.debian.org/debian unstable/main amd64 libmagickcore-7.q16-10 amd64 8:7.1.1.43+dfsg1-1 [1843 kB]
Get: 47 http://deb.debian.org/debian unstable/main amd64 libmagickwand-7.q16-10 amd64 8:7.1.1.43+dfsg1-1 [340 kB]
Get: 48 http://deb.debian.org/debian unstable/main amd64 poppler-data all 0.4.12-1 [1601 kB]
Get: 49 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.2-2 [859 kB]
Get: 50 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.2-2 [2210 kB]
Get: 51 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.2-2 [27.1 kB]
Get: 52 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB]
Get: 53 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB]
Get: 54 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025b-1 [259 kB]
Get: 55 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB]
Get: 56 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB]
Get: 57 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.2-2 [1952 kB]
Get: 58 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.2-2 [746 kB]
Get: 59 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.2-2 [10.1 kB]
Get: 60 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.2-2 [28.1 kB]
Get: 61 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB]
Get: 62 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-7 [64.9 kB]
Get: 63 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-7 [878 kB]
Get: 64 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 65 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-3 [337 kB]
Get: 66 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-3 [109 kB]
Get: 67 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-3 [43.5 kB]
Get: 68 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
Get: 69 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 70 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 71 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB]
Get: 72 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 73 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 74 http://deb.debian.org/debian unstable/main amd64 libtext-charwidth-perl amd64 0.04-11+b4 [9476 B]
Get: 75 http://deb.debian.org/debian unstable/main amd64 libtext-wrapi18n-perl all 0.06-10 [8808 B]
Get: 76 http://deb.debian.org/debian unstable/main amd64 ucf all 3.0050 [42.7 kB]
Get: 77 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB]
Get: 78 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB]
Get: 79 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB]
Get: 80 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB]
Get: 81 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 82 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB]
Get: 83 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 84 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 85 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 86 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 87 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 88 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 89 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB]
Get: 90 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get: 91 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 92 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 93 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB]
Get: 94 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB]
Get: 95 http://deb.debian.org/debian unstable/main amd64 sgml-data all 2.0.11+nmu1 [179 kB]
Get: 96 http://deb.debian.org/debian unstable/main amd64 docbook all 4.5-11 [126 kB]
Get: 97 http://deb.debian.org/debian unstable/main amd64 libosp5 amd64 1.5.2-15.2 [972 kB]
Get: 98 http://deb.debian.org/debian unstable/main amd64 opensp amd64 1.5.2-15.2 [448 kB]
Get: 99 http://deb.debian.org/debian unstable/main amd64 docbook-to-man amd64 1:2.0.0-48 [74.2 kB]
Get: 100 http://deb.debian.org/debian unstable/main amd64 fonts-lmodern all 2.005-1 [4540 kB]
Get: 101 http://deb.debian.org/debian unstable/main amd64 libgs-common all 10.05.0~dfsg-1 [148 kB]
Get: 102 http://deb.debian.org/debian unstable/main amd64 libgs10-common all 10.05.0~dfsg-1 [476 kB]
Get: 103 http://deb.debian.org/debian unstable/main amd64 libavahi-common-data amd64 0.8-16 [112 kB]
Get: 104 http://deb.debian.org/debian unstable/main amd64 libavahi-common3 amd64 0.8-16 [44.2 kB]
Get: 105 http://deb.debian.org/debian unstable/main amd64 libdbus-1-3 amd64 1.16.2-2 [178 kB]
Get: 106 http://deb.debian.org/debian unstable/main amd64 libavahi-client3 amd64 0.8-16 [48.4 kB]
Get: 107 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB]
Get: 108 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB]
Get: 109 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB]
Get: 110 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB]
Get: 111 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB]
Get: 112 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1+b1 [24.3 kB]
Get: 113 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB]
Get: 114 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B]
Get: 115 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB]
Get: 116 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB]
Get: 117 http://deb.debian.org/debian unstable/main amd64 libcups2t64 amd64 2.4.10-2+b1 [251 kB]
Get: 118 http://deb.debian.org/debian unstable/main amd64 libidn12 amd64 1.43-1 [47.7 kB]
Get: 119 http://deb.debian.org/debian unstable/main amd64 libijs-0.35 amd64 0.35-15.2 [14.8 kB]
Get: 120 http://deb.debian.org/debian unstable/main amd64 libjbig2dec0 amd64 0.20-1+b3 [65.1 kB]
Get: 121 http://deb.debian.org/debian unstable/main amd64 libpaper2 amd64 2.2.5-0.3+b1 [16.6 kB]
Get: 122 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB]
Get: 123 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.6-1 [37.3 kB]
Get: 124 http://deb.debian.org/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b2 [188 kB]
Get: 125 http://deb.debian.org/debian unstable/main amd64 libgs10 amd64 10.05.0~dfsg-1 [2567 kB]
Get: 126 http://deb.debian.org/debian unstable/main amd64 ghostscript amd64 10.05.0~dfsg-1 [49.9 kB]
Get: 127 http://deb.debian.org/debian unstable/main amd64 native-architecture all 0.2.6 [2264 B]
Get: 128 http://deb.debian.org/debian unstable/main amd64 libgirepository-2.0-0 amd64 2.84.0-2 [141 kB]
Get: 129 http://deb.debian.org/debian unstable/main amd64 girepository-tools amd64 2.84.0-2 [148 kB]
Get: 130 http://deb.debian.org/debian unstable/main amd64 libnetpbm11t64 amd64 2:11.09.03-1 [184 kB]
Get: 131 http://deb.debian.org/debian unstable/main amd64 netpbm amd64 2:11.09.03-1 [2081 kB]
Get: 132 http://deb.debian.org/debian unstable/main amd64 tex-common all 6.19 [29.4 kB]
Get: 133 http://deb.debian.org/debian unstable/main amd64 libpaper-utils amd64 2.2.5-0.3+b1 [16.4 kB]
Get: 134 http://deb.debian.org/debian unstable/main amd64 libkpathsea6 amd64 2024.20240313.70630+ds-6 [157 kB]
Get: 135 http://deb.debian.org/debian unstable/main amd64 libptexenc1 amd64 2024.20240313.70630+ds-6 [49.3 kB]
Get: 136 http://deb.debian.org/debian unstable/main amd64 libsynctex2 amd64 2024.20240313.70630+ds-6 [62.9 kB]
Get: 137 http://deb.debian.org/debian unstable/main amd64 libtexlua53-5 amd64 2024.20240313.70630+ds-6 [114 kB]
Get: 138 http://deb.debian.org/debian unstable/main amd64 t1utils amd64 1.41-4 [62.1 kB]
Get: 139 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB]
Get: 140 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB]
Get: 141 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB]
Get: 142 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.12-1 [27.9 kB]
Get: 143 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.4-1+b1 [538 kB]
Get: 144 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB]
Get: 145 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 10.2.0-1+b1 [479 kB]
Get: 146 http://deb.debian.org/debian unstable/main amd64 libicu76 amd64 76.1-3 [9721 kB]
Get: 147 http://deb.debian.org/debian unstable/main amd64 libmpfi0 amd64 1.5.4+ds-4 [35.5 kB]
Get: 148 http://deb.debian.org/debian unstable/main amd64 libpotrace0 amd64 1.16-2+b2 [25.6 kB]
Get: 149 http://deb.debian.org/debian unstable/main amd64 libteckit0 amd64 2.5.12+ds1-1+b1 [341 kB]
Get: 150 http://deb.debian.org/debian unstable/main amd64 libxmu6 amd64 2:1.1.3-3+b4 [59.0 kB]
Get: 151 http://deb.debian.org/debian unstable/main amd64 libxpm4 amd64 1:3.5.17-1+b3 [56.2 kB]
Get: 152 http://deb.debian.org/debian unstable/main amd64 libxaw7 amd64 2:1.0.16-1 [212 kB]
Get: 153 http://deb.debian.org/debian unstable/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB]
Get: 154 http://deb.debian.org/debian unstable/main amd64 libzzip-0-13t64 amd64 0.13.78+dfsg.1-0.1 [59.0 kB]
Get: 155 http://deb.debian.org/debian unstable/main amd64 texlive-binaries amd64 2024.20240313.70630+ds-6 [8446 kB]
Get: 156 http://deb.debian.org/debian unstable/main amd64 xdg-utils all 1.2.1-2 [75.8 kB]
Get: 157 http://deb.debian.org/debian unstable/main amd64 texlive-base all 2024.20250309-1 [23.1 MB]
Get: 158 http://deb.debian.org/debian unstable/main amd64 hicolor-icon-theme all 0.18-2 [11.8 kB]
Get: 159 http://deb.debian.org/debian unstable/main amd64 imagemagick-7.q16 amd64 8:7.1.1.43+dfsg1-1 [726 kB]
Get: 160 http://deb.debian.org/debian unstable/main amd64 imagemagick amd64 8:7.1.1.43+dfsg1-1 [20.0 kB]
Get: 161 http://deb.debian.org/debian unstable/main amd64 hevea amd64 2.36-2+b3 [2073 kB]
Get: 162 http://deb.debian.org/debian unstable/main amd64 uuid-dev amd64 2.40.4-5 [47.8 kB]
Get: 163 http://deb.debian.org/debian unstable/main amd64 libblkid-dev amd64 2.40.4-5 [205 kB]
Get: 164 http://deb.debian.org/debian unstable/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB]
Get: 165 http://deb.debian.org/debian unstable/main amd64 libffi-dev amd64 3.4.7-1 [60.8 kB]
Get: 166 http://deb.debian.org/debian unstable/main amd64 libfile-which-perl all 1.27-2 [15.1 kB]
Get: 167 http://deb.debian.org/debian unstable/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB]
Get: 168 http://deb.debian.org/debian unstable/main amd64 libfl2 amd64 2.6.4-8.2+b4 [84.3 kB]
Get: 169 http://deb.debian.org/debian unstable/main amd64 libfl-dev amd64 2.6.4-8.2+b4 [85.6 kB]
Get: 170 http://deb.debian.org/debian unstable/main amd64 libsepol-dev amd64 3.8.1-1 [373 kB]
Get: 171 http://deb.debian.org/debian unstable/main amd64 libpcre2-16-0 amd64 10.45-1 [281 kB]
Get: 172 http://deb.debian.org/debian unstable/main amd64 libpcre2-32-0 amd64 10.45-1 [268 kB]
Get: 173 http://deb.debian.org/debian unstable/main amd64 libpcre2-posix3 amd64 10.45-1 [63.5 kB]
Get: 174 http://deb.debian.org/debian unstable/main amd64 libpcre2-dev amd64 10.45-1 [853 kB]
Get: 175 http://deb.debian.org/debian unstable/main amd64 libselinux1-dev amd64 3.8.1-1 [169 kB]
Get: 176 http://deb.debian.org/debian unstable/main amd64 libmount-dev amd64 2.40.4-5 [29.6 kB]
Get: 177 http://deb.debian.org/debian unstable/main amd64 libsysprof-capture-4-dev amd64 48.0-2 [49.9 kB]
Get: 178 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB]
Get: 179 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB]
Get: 180 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB]
Get: 181 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB]
Get: 182 http://deb.debian.org/debian unstable/main amd64 libgio-2.0-dev amd64 2.84.0-2 [1685 kB]
Get: 183 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.2-1 [55.3 kB]
Get: 184 http://deb.debian.org/debian unstable/main amd64 libgio-2.0-dev-bin amd64 2.84.0-2 [164 kB]
Get: 185 http://deb.debian.org/debian unstable/main amd64 libglib2.0-data all 2.84.0-2 [1286 kB]
Get: 186 http://deb.debian.org/debian unstable/main amd64 libglib2.0-bin amd64 2.84.0-2 [128 kB]
Get: 187 http://deb.debian.org/debian unstable/main amd64 libglib2.0-dev-bin amd64 2.84.0-2 [52.9 kB]
Get: 188 http://deb.debian.org/debian unstable/main amd64 libglib2.0-dev amd64 2.84.0-2 [53.6 kB]
Get: 189 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 190 http://deb.debian.org/debian unstable/main amd64 libmime-charset-perl all 1.013.1-2 [34.0 kB]
Get: 191 http://deb.debian.org/debian unstable/main amd64 libthai-data all 0.1.29-2 [168 kB]
Get: 192 http://deb.debian.org/debian unstable/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB]
Get: 193 http://deb.debian.org/debian unstable/main amd64 libsombok3 amd64 2.4.0-2+b2 [31.8 kB]
Get: 194 http://deb.debian.org/debian unstable/main amd64 libunicode-linebreak-perl amd64 0.0.20190101-1+b9 [96.1 kB]
Get: 195 http://deb.debian.org/debian unstable/main amd64 libyaml-tiny-perl all 1.76-1 [29.8 kB]
Get: 196 http://deb.debian.org/debian unstable/main amd64 lmodern all 2.005-1 [9480 kB]
Get: 197 http://deb.debian.org/debian unstable/main amd64 texlive-latex-base all 2024.20250309-1 [1294 kB]
Get: 198 http://deb.debian.org/debian unstable/main amd64 texlive-luatex all 2024.20250309-1 [29.1 MB]
Get: 199 http://deb.debian.org/debian unstable/main amd64 texlive-plain-generic all 2024.20250309-2 [29.0 MB]
Get: 200 http://deb.debian.org/debian unstable/main amd64 texlive-extra-utils all 2024.20250309-2 [67.6 MB]
Fetched 253 MB in 6s (40.9 MB/s)
Preconfiguring packages ...
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(Reading database ... 19805 files and directories currently installed.)
Preparing to unpack .../00-m4_1.4.19-7_amd64.deb ...
Unpacking m4 (1.4.19-7) ...
Selecting previously unselected package flex.
Preparing to unpack .../01-flex_2.6.4-8.2+b4_amd64.deb ...
Unpacking flex (2.6.4-8.2+b4) ...
Selecting previously unselected package libfftw3-double3:amd64.
Preparing to unpack .../02-libfftw3-double3_3.3.10-2+b1_amd64.deb ...
Unpacking libfftw3-double3:amd64 (3.3.10-2+b1) ...
Selecting previously unselected package libexpat1:amd64.
Preparing to unpack .../03-libexpat1_2.7.1-1_amd64.deb ...
Unpacking libexpat1:amd64 (2.7.1-1) ...
Selecting previously unselected package libbrotli1:amd64.
Preparing to unpack .../04-libbrotli1_1.1.0-2+b7_amd64.deb ...
Unpacking libbrotli1:amd64 (1.1.0-2+b7) ...
Selecting previously unselected package libpng16-16t64:amd64.
Preparing to unpack .../05-libpng16-16t64_1.6.47-1.1_amd64.deb ...
Unpacking libpng16-16t64:amd64 (1.6.47-1.1) ...
Selecting previously unselected package libfreetype6:amd64.
Preparing to unpack .../06-libfreetype6_2.13.3+dfsg-1_amd64.deb ...
Unpacking libfreetype6:amd64 (2.13.3+dfsg-1) ...
Selecting previously unselected package fonts-dejavu-mono.
Preparing to unpack .../07-fonts-dejavu-mono_2.37-8_all.deb ...
Unpacking fonts-dejavu-mono (2.37-8) ...
Selecting previously unselected package fonts-dejavu-core.
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Unpacking fonts-dejavu-core (2.37-8) ...
Selecting previously unselected package libfontenc1:amd64.
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Unpacking libfontenc1:amd64 (1:1.1.8-1+b2) ...
Selecting previously unselected package x11-common.
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Unpacking x11-common (1:7.7+24) ...
Selecting previously unselected package xfonts-encodings.
Preparing to unpack .../11-xfonts-encodings_1%3a1.0.4-2.2_all.deb ...
Unpacking xfonts-encodings (1:1.0.4-2.2) ...
Selecting previously unselected package xfonts-utils.
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Unpacking xfonts-utils (1:7.7+7) ...
Selecting previously unselected package fonts-urw-base35.
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Unpacking fonts-urw-base35 (20200910-8) ...
Selecting previously unselected package fontconfig-config.
Preparing to unpack .../14-fontconfig-config_2.15.0-2.2_amd64.deb ...
Unpacking fontconfig-config (2.15.0-2.2) ...
Selecting previously unselected package libfontconfig1:amd64.
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Unpacking libfontconfig1:amd64 (2.15.0-2.2) ...
Selecting previously unselected package libsharpyuv0:amd64.
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Unpacking libsharpyuv0:amd64 (1.5.0-0.1) ...
Selecting previously unselected package libdav1d7:amd64.
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Unpacking libdav1d7:amd64 (1.5.1-1) ...
Selecting previously unselected package libheif-plugin-dav1d:amd64.
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Unpacking libheif-plugin-dav1d:amd64 (1.19.7-1) ...
Selecting previously unselected package libde265-0:amd64.
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Unpacking libde265-0:amd64 (1.0.15-1+b3) ...
Selecting previously unselected package libheif-plugin-libde265:amd64.
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Unpacking libheif-plugin-libde265:amd64 (1.19.7-1) ...
Selecting previously unselected package libheif1:amd64.
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Unpacking libheif1:amd64 (1.19.7-1) ...
Selecting previously unselected package libjbig0:amd64.
Preparing to unpack .../22-libjbig0_2.1-6.1+b2_amd64.deb ...
Unpacking libjbig0:amd64 (2.1-6.1+b2) ...
Selecting previously unselected package libjpeg62-turbo:amd64.
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Unpacking libjpeg62-turbo:amd64 (1:2.1.5-3.1) ...
Selecting previously unselected package liblcms2-2:amd64.
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Unpacking liblcms2-2:amd64 (2.16-2) ...
Selecting previously unselected package libffi8:amd64.
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Current default time zone: 'Etc/UTC'
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I: Building the package
I: Running cd /build/reproducible-path/wise-2.4.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S  > ../wise_2.4.1-27_source.changes
dpkg-buildpackage: info: source package wise
dpkg-buildpackage: info: source version 2.4.1-27
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Lance Lin <lq27267@gmail.com>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
 debian/rules clean
dh clean
   debian/rules override_dh_clean
make[1]: Entering directory '/build/reproducible-path/wise-2.4.1'
/usr/bin/make -C src clean
make[2]: Entering directory '/build/reproducible-path/wise-2.4.1/src'
cd external ; /usr/bin/make clean
make[3]: Entering directory '/build/reproducible-path/wise-2.4.1/src/external'
(cd mott; make clean)
make[4]: Entering directory '/build/reproducible-path/wise-2.4.1/src/external/mott'
rm -f *.[oa]
make[4]: Leaving directory '/build/reproducible-path/wise-2.4.1/src/external/mott'
make[3]: Leaving directory '/build/reproducible-path/wise-2.4.1/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 '/build/reproducible-path/wise-2.4.1/src'
/usr/bin/make -C debian/manpages.d clean
make[2]: Entering directory '/build/reproducible-path/wise-2.4.1/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 '/build/reproducible-path/wise-2.4.1/debian/manpages.d'
rm -f -r src/oldbin
for i in dba psw dnal genomewise pswdb scanwise estwise genewise sywise genewisedb promoterwise pseudowise estwisedb; do rm -f src/models/$i; done
rm -f src/network/scanwise_server
rm -f docs/temp.tex
rm -f docs/api.*
rm -f docs/wise2.image.tex
rm -f docs/*.pdf
rm -f docs/*.aux
rm -f docs/*.log
rm -f docs/*.toc
rm -f docs/*.pdf
rm -f docs/*.dvi
rm -f docs/*.ps
rm -f docs/*.4ct
rm -f docs/*.4tc
rm -f docs/*.css
rm -f docs/*.idv
rm -f docs/*.lg
rm -f docs/*.tmp
rm -f docs/*.xref
rm -f docs/*.haux
rm -f docs/*.htoc
rm -f docs/*.html
rm -f -r docs/api
rm -f -r docs/dynamite
rm -f -r docs/wise2
dh_clean
	rm -f debian/debhelper-build-stamp
	rm -rf debian/.debhelper/
	rm -f -- debian/wise.substvars debian/wise-doc.substvars debian/wise-data.substvars debian/files
	rm -fr -- debian/wise/ debian/tmp/ debian/wise-doc/ debian/wise-data/
	find .  \( \( \
		\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \
	        \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
		 -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
		 -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
		 -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
		\) -exec rm -f {} + \) -o \
		\( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \)
make[1]: Leaving directory '/build/reproducible-path/wise-2.4.1'
 debian/rules binary
dh binary
   dh_update_autotools_config
   dh_autoreconf
   debian/rules override_dh_auto_build
make[1]: Entering directory '/build/reproducible-path/wise-2.4.1'
# The dyc compiler is needed before building the all the rest.
# Also, it pre-depends on the libwisebase library, otherwise
# linking fails.
dh_auto_build --sourcedirectory=src/base -- libwisebase.a
	cd src/base && make -j42 "INSTALL=install --strip-program=true" libwisebase.a
make[2]: Entering directory '/build/reproducible-path/wise-2.4.1/src/base'
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wiseconfig.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wisestring.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wiseerror.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wisememman.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wisefile.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wiserandom.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wisetime.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wiseoverlay.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread wisestreaminterface.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread commandline.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c -DUNIX -pthread linesubs.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 *
ar ru libwisebase.a wiseconfig.o wisestring.o wiseerror.o wisememman.o wisefile.o wiserandom.o wisetime.o wiseoverlay.o wisestreaminterface.o commandline.o linesubs.o
ar: `u' modifier ignored since `D' is the default (see `U')
ar: creating libwisebase.a
if test -x /bin/ranlib; then /bin/ranlib libwisebase.a; else exit 0; fi
if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisebase.a; else exit 0; fi
make[2]: Leaving directory '/build/reproducible-path/wise-2.4.1/src/base'
dh_auto_build --sourcedirectory=src/dyc -- dyc
	cd src/dyc && make -j42 "INSTALL=install --strip-program=true" dyc
make[2]: Entering directory '/build/reproducible-path/wise-2.4.1/src/dyc'
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g  -DUNIX  -I../base/ -I../base/ dyc.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g  -DUNIX  -I../base/ -I../base/ dyna2.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g  -DUNIX  -I../base/ -I../base/ dynfile.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g  -DUNIX  -I../base/ -I../base/ wisec.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g  -DUNIX  -I../base/ -I../base/ dynafunc.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g  -DUNIX  -I../base/ -I../base/ module.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g  -DUNIX  -I../base/ -I../base/ type.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g  -DUNIX  -I../base/ -I../base/ method.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g  -DUNIX  -I../base/ -I../base/ dynadb.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g  -DUNIX  -I../base/ -I../base/ friend.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g  -DUNIX  -I../base/ -I../base/ inputfile.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g  -DUNIX  -I../base/ -I../base/ variable.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g  -DUNIX  -I../base/ -I../base/ modulefunc.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g  -DUNIX  -I../base/ -I../base/ api.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g  -DUNIX  -I../base/ -I../base/ display.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g  -DUNIX  -I../base/ -I../base/ dynashadow.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g  -DUNIX  -I../base/ -I../base/ labelmaster.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g  -DUNIX  -I../base/ -I../base/ ftext.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g  -DUNIX  -I../base/ -I../base/ funcinfo.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g  -DUNIX  -I../base/ -I../base/ objectinfo.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g  -DUNIX  -I../base/ -I../base/ exprtree.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g  -DUNIX  -I../base/ -I../base/ compugen.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g  -DUNIX  -I../base/ -I../base/ docugen.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g  -DUNIX  -I../base/ -I../base/ input.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g  -DUNIX  -I../base/ -I../base/ dpimpl.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g  -DUNIX  -I../base/ -I../base/ dbthread.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g  -DUNIX  -I../base/ -I../base/ probal.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g  -DUNIX  -I../base/ -I../base/ telegraph.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g  -DUNIX  -I../base/ -I../base/ dynadebug.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g  -DUNIX  -I../base/ -I../base/ dyshatter.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g  -DUNIX  -I../base/ -I../base/ y.tab.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -c -g  -DUNIX  -I../base/ -I../base/ lex.yy.c
dynashadow.dy: In function ‘optimised_shadow_GenericMatrix’:
dynashadow.dy:2180:31: warning: passing argument 2 of ‘write_main_shadow_block’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
 2180 |   write_main_shadow_block(dfp,gm,"DC_OPT_SHADOW_MATRIX","mat","DC_OPT_SHADOW_SPECIAL","DC_OPT_SHADOW_MATRIX_SP","DC_OPT_SHADOW_SPECIAL_SP",7,TRUE,TRUE,0,TRUE);
      |                               ^~
In file included from dynashadow.c:4:
dynashadow.h:163:60: note: expected ‘GenericMatrix *’ but argument is of type ‘const GenericMatrix *’
  163 | void write_main_shadow_block(DYNFILE * dfp,GenericMatrix * gm,char * matrixtag,char * pointer_tag,char * specialtag,char * shadow_main_tag,char * shadow_special_tag,int shadow_length,boolean shadow_on_special,boolean use_special,int debug,int use_shadow_pointer);
      |                                            ~~~~~~~~~~~~~~~~^~
dynashadow.dy:2187:36: warning: passing argument 2 of ‘write_special_shadow_block’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers]
 2187 |     write_special_shadow_block(dfp,gm,"DC_OPT_SHADOW_MATRIX","mat","DC_OPT_SHADOW_SPECIAL","DC_OPT_SHADOW_MATRIX_SP","DC_OPT_SHADOW_SPECIAL_SP",7,TRUE,0);
      |                                    ^~
dynashadow.h:189:63: note: expected ‘GenericMatrix *’ but argument is of type ‘const GenericMatrix *’
  189 | void write_special_shadow_block(DYNFILE * dfp,GenericMatrix * gm,char * matrix,char * pointer_tag,char * special,char *  shadow_main_tag,char * shadow_special_tag,int shadow_length,boolean shadow_on_special,int debug);
      |                                               ~~~~~~~~~~~~~~~~^~
dynfile.dy: In function ‘warn_expr’:
dynfile.dy:699:16: warning: ‘%s’ directive writing up to 511 bytes into a region of size 506 [-Wformat-overflow=]
  699 |   sprintf(buf2,"warn(\"%s\");",buffer);
      |                ^~~~~~~~~~~~~~~ ~~~~~~
In file included from /usr/include/stdio.h:970,
                 from ../base/wisebase.h:6,
                 from dynfile.h:6,
                 from dynfile.c:4:
In function ‘sprintf’,
    inlined from ‘warn_expr’ at dynfile.dy:699:3:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 10 and 521 bytes into a destination of size 512
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
cc -o dyc dyc.o dyna2.o dynfile.o wisec.o dynafunc.o module.o type.o method.o dynadb.o friend.o inputfile.o variable.o modulefunc.o api.o display.o dynashadow.o labelmaster.o ftext.o funcinfo.o objectinfo.o exprtree.o compugen.o docugen.o input.o dpimpl.o dbthread.o probal.o telegraph.o dynadebug.o dyshatter.o y.tab.o lex.yy.o  -ll -lwisebase -Wl,-z,relro -Wl,-z,now -g  -lm -L../base/ -lpthread
make[2]: Leaving directory '/build/reproducible-path/wise-2.4.1/src/dyc'
PATH="$PATH:/build/reproducible-path/wise-2.4.1/src/dyc" \
dh_auto_build --sourcedirectory=src -- all
	cd src && make -j42 "INSTALL=install --strip-program=true" all
make[2]: Entering directory '/build/reproducible-path/wise-2.4.1/src'
(cd base   ; make CC="cc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  `pkg-config --cflags glib-2.0`" libwisebase.a )
make[3]: Entering directory '/build/reproducible-path/wise-2.4.1/src/base'
make[3]: 'libwisebase.a' is up to date.
make[3]: Leaving directory '/build/reproducible-path/wise-2.4.1/src/base'
(cd HMMer2 ; make CC="cc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  `pkg-config --cflags glib-2.0`" libhmmer.a )
make[3]: Entering directory '/build/reproducible-path/wise-2.4.1/src/HMMer2'
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c alphabet.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c core_algorithms.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c debug.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c emit.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c emulation.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c histogram.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c hmmio.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c mathsupport.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c masks.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c misc.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c modelmakers.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c plan7.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c plan9.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c prior.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c tophits.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c trace.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c aligneval.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c alignio.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c cluster.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c dayhoff.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c file.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c getopt.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c gnuregex.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c interleaved.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c iupac.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c msf.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c revcomp.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c selex.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c sqerror.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c sqio.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c sre_ctype.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c sre_math.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c sre_string.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c stack.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c translate.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c types.c		
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread   -c weight.c		
gnuregex.c: In function ‘re_match_2’:
gnuregex.c:3755:31: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 3755 |                           if ((int) old_regend[r] >= (int) regstart[r])
      |                               ^
gnuregex.c:3755:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 3755 |                           if ((int) old_regend[r] >= (int) regstart[r])
      |                                                      ^
gnuregex.c:2316:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
 2316 |   fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
      |                                          ^
gnuregex.c:2395:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
 2395 |     PUSH_FAILURE_ITEM (lowest_active_reg);                              \
      |     ^~~~~~~~~~~~~~~~~
gnuregex.c:3761:19: note: in expansion of macro ‘PUSH_FAILURE_POINT’
 3761 |                   PUSH_FAILURE_POINT (p1 + mcnt, d, -2);
      |                   ^~~~~~~~~~~~~~~~~~
gnuregex.c:2316:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
 2316 |   fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
      |                                          ^
gnuregex.c:2398:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
 2398 |     PUSH_FAILURE_ITEM (highest_active_reg);                             \
      |     ^~~~~~~~~~~~~~~~~
gnuregex.c:3761:19: note: in expansion of macro ‘PUSH_FAILURE_POINT’
 3761 |                   PUSH_FAILURE_POINT (p1 + mcnt, d, -2);
      |                   ^~~~~~~~~~~~~~~~~~
gnuregex.c:2316:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
 2316 |   fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
      |                                          ^
gnuregex.c:2395:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
 2395 |     PUSH_FAILURE_ITEM (lowest_active_reg);                              \
      |     ^~~~~~~~~~~~~~~~~
gnuregex.c:3908:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’
 3908 |           PUSH_FAILURE_POINT (p + mcnt, NULL, -2);
      |           ^~~~~~~~~~~~~~~~~~
gnuregex.c:2316:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
 2316 |   fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
      |                                          ^
gnuregex.c:2398:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
 2398 |     PUSH_FAILURE_ITEM (highest_active_reg);                             \
      |     ^~~~~~~~~~~~~~~~~
gnuregex.c:3908:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’
 3908 |           PUSH_FAILURE_POINT (p + mcnt, NULL, -2);
      |           ^~~~~~~~~~~~~~~~~~
gnuregex.c:2316:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
 2316 |   fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
      |                                          ^
gnuregex.c:2395:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
 2395 |     PUSH_FAILURE_ITEM (lowest_active_reg);                              \
      |     ^~~~~~~~~~~~~~~~~
gnuregex.c:3961:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’
 3961 |           PUSH_FAILURE_POINT (p + mcnt, d, -2);
      |           ^~~~~~~~~~~~~~~~~~
gnuregex.c:2316:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
 2316 |   fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
      |                                          ^
gnuregex.c:2398:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
 2398 |     PUSH_FAILURE_ITEM (highest_active_reg);                             \
      |     ^~~~~~~~~~~~~~~~~
gnuregex.c:3961:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’
 3961 |           PUSH_FAILURE_POINT (p + mcnt, d, -2);
      |           ^~~~~~~~~~~~~~~~~~
gnuregex.c:2483:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 2483 |   high_reg = (unsigned) POP_FAILURE_ITEM ();                            \
      |              ^
gnuregex.c:4067:13: note: in expansion of macro ‘POP_FAILURE_POINT’
 4067 |             POP_FAILURE_POINT (sdummy, pdummy,
      |             ^~~~~~~~~~~~~~~~~
gnuregex.c:2486:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 2486 |   low_reg = (unsigned) POP_FAILURE_ITEM ();                             \
      |             ^
gnuregex.c:4067:13: note: in expansion of macro ‘POP_FAILURE_POINT’
 4067 |             POP_FAILURE_POINT (sdummy, pdummy,
      |             ^~~~~~~~~~~~~~~~~
gnuregex.c:2316:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
 2316 |   fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
      |                                          ^
gnuregex.c:2395:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
 2395 |     PUSH_FAILURE_ITEM (lowest_active_reg);                              \
      |     ^~~~~~~~~~~~~~~~~
gnuregex.c:4100:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’
 4100 |           PUSH_FAILURE_POINT (0, 0, -2);
      |           ^~~~~~~~~~~~~~~~~~
gnuregex.c:2316:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
 2316 |   fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
      |                                          ^
gnuregex.c:2398:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
 2398 |     PUSH_FAILURE_ITEM (highest_active_reg);                             \
      |     ^~~~~~~~~~~~~~~~~
gnuregex.c:4100:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’
 4100 |           PUSH_FAILURE_POINT (0, 0, -2);
      |           ^~~~~~~~~~~~~~~~~~
gnuregex.c:2316:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
 2316 |   fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
      |                                          ^
gnuregex.c:2395:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
 2395 |     PUSH_FAILURE_ITEM (lowest_active_reg);                              \
      |     ^~~~~~~~~~~~~~~~~
gnuregex.c:4113:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’
 4113 |           PUSH_FAILURE_POINT (0, 0, -2);
      |           ^~~~~~~~~~~~~~~~~~
gnuregex.c:2316:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast]
 2316 |   fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item
      |                                          ^
gnuregex.c:2398:5: note: in expansion of macro ‘PUSH_FAILURE_ITEM’
 2398 |     PUSH_FAILURE_ITEM (highest_active_reg);                             \
      |     ^~~~~~~~~~~~~~~~~
gnuregex.c:4113:11: note: in expansion of macro ‘PUSH_FAILURE_POINT’
 4113 |           PUSH_FAILURE_POINT (0, 0, -2);
      |           ^~~~~~~~~~~~~~~~~~
gnuregex.c:2483:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 2483 |   high_reg = (unsigned) POP_FAILURE_ITEM ();                            \
      |              ^
gnuregex.c:4281:11: note: in expansion of macro ‘POP_FAILURE_POINT’
 4281 |           POP_FAILURE_POINT (d, p,
      |           ^~~~~~~~~~~~~~~~~
gnuregex.c:2486:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
 2486 |   low_reg = (unsigned) POP_FAILURE_ITEM ();                             \
      |             ^
gnuregex.c:4281:11: note: in expansion of macro ‘POP_FAILURE_POINT’
 4281 |           POP_FAILURE_POINT (d, p,
      |           ^~~~~~~~~~~~~~~~~
cluster.c: In function ‘Cluster’:
cluster.c:178:26: warning: argument 1 range [18446744065119617024, 18446744073709551612] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  178 |       (diff  = (float *) malloc ((N-1) * sizeof(float))) == NULL)
      |                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from squid.h:22,
                 from cluster.c:122:
/usr/include/stdlib.h:672:14: note: in a call to allocation function ‘malloc’ declared here
  672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__
      |              ^~~~~~
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 '/build/reproducible-path/wise-2.4.1/src/HMMer2'
(cd dynlibsrc ; make CC="cc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  `pkg-config --cflags glib-2.0`" libdyna.a )
make[3]: Entering directory '/build/reproducible-path/wise-2.4.1/src/dynlibsrc'
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ packaln.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ aln.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ dnamatrix.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ probability.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ alnrange.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ alnconvert.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ basematrix.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ shattermatrix.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ matrixdebug.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ dpenvelope.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ dbsearchimpl.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ dprunimpl.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ complexsequence.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ complexevalset.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ complexconsensi.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ sequence.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ sequencestream.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ seqalign.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ hitlist.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ hsp.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ hspstream.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ codon.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ compmat.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ codonmatrix.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ codonmapper.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ sequencedb.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ hscore.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ seqlookup.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ arrayseqlookup.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ genericindexresult.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ linkedlist_lookpos.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ singlenumberspace.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ histogram.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ searchstatinterface.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ searchstatlookup.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ proteindb.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ protein.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ pairbase.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ pairbaseseq.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ genomicdb.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ randommodel.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ randomdb.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);
      |                   ^~~~~~~~~~~~
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);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~
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);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ genomic.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ cdna.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ cdnadb.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ dna.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ embl.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ genomicregion.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ gene.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ transcript.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ translation.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ btcanvas.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ asciibtcanvas.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ dynlibcross.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);
      |   ^~~~~~~~~~~~~~~~~~~~~~~~
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 '/build/reproducible-path/wise-2.4.1/src/dynlibsrc'
(cd dynlibsrc ; make CC="cc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  `pkg-config --cflags glib-2.0`" libdyna_glib.a )
make[3]: Entering directory '/build/reproducible-path/wise-2.4.1/src/dynlibsrc'
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ subseqhash.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ intallocator.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ proteinstreamedindex.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ shadowseq.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ shadowseqindex.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ hsphandler.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ hspscaninterface.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ hsp2hitscan.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ hsplookupscan.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ hsplookupthreaded.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ hspthreadeddb.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ hspscanruntime.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ hsptwohitscan.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ proteinindexcons.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ dnaindexcons.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ staticseq.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 *
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
hsp2hitscan.dy: In function ‘Wise2_one_off_two_hit_HSPscan_query_direct’:
hsp2hitscan.dy:209:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘__time_t’ {aka ‘long int’} [-Wformat=]
  209 |   fprintf(stderr,"START %d.%03du %d.%03ds \n",
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
  210 |           use.ru_utime.tv_sec,
      |           ~~~~~~~~~~~~~~~~~~~
      |                       |
      |                       __time_t {aka long int}
hsp2hitscan.dy:209:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘__time_t’ {aka ‘long int’} [-Wformat=]
  209 |   fprintf(stderr,"START %d.%03du %d.%03ds \n",
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
  210 |           use.ru_utime.tv_sec,
  211 |           use.ru_utime.tv_sec/1000,
      |           ~~~~~~~~~~~~~~~~~~~~~~~~
      |                              |
      |                              __time_t {aka long int}
hsp2hitscan.dy:209:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘__time_t’ {aka ‘long int’} [-Wformat=]
  209 |   fprintf(stderr,"START %d.%03du %d.%03ds \n",
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
  212 |           use.ru_stime.tv_sec,
      |           ~~~~~~~~~~~~~~~~~~~
      |                       |
      |                       __time_t {aka long int}
hsp2hitscan.dy:209:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘__time_t’ {aka ‘long int’} [-Wformat=]
  209 |   fprintf(stderr,"START %d.%03du %d.%03ds \n",
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
  213 |           use.ru_stime.tv_sec/1000
      |           ~~~~~~~~~~~~~~~~~~~~~~~~
      |                              |
      |                              __time_t {aka long int}
hsp2hitscan.dy:273:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘__time_t’ {aka ‘long int’} [-Wformat=]
  273 |   fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n",
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  274 |           use.ru_utime.tv_sec,
      |           ~~~~~~~~~~~~~~~~~~~
      |                       |
      |                       __time_t {aka long int}
hsp2hitscan.dy:273:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘__time_t’ {aka ‘long int’} [-Wformat=]
  273 |   fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n",
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  274 |           use.ru_utime.tv_sec,
  275 |           use.ru_utime.tv_sec/1000,
      |           ~~~~~~~~~~~~~~~~~~~~~~~~
      |                              |
      |                              __time_t {aka long int}
hsp2hitscan.dy:273:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘__time_t’ {aka ‘long int’} [-Wformat=]
  273 |   fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n",
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
  276 |           use.ru_stime.tv_sec,
      |           ~~~~~~~~~~~~~~~~~~~
      |                       |
      |                       __time_t {aka long int}
hsp2hitscan.dy:273:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘__time_t’ {aka ‘long int’} [-Wformat=]
  273 |   fprintf(stderr,"END OF SEED %d.%03du %d.%03ds \n",
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
  277 |           use.ru_stime.tv_sec/1000
      |           ~~~~~~~~~~~~~~~~~~~~~~~~
      |                              |
      |                              __time_t {aka long int}
hsp2hitscan.dy:286:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘__time_t’ {aka ‘long int’} [-Wformat=]
  286 |   fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n",
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  287 |           use.ru_utime.tv_sec,
      |           ~~~~~~~~~~~~~~~~~~~
      |                       |
      |                       __time_t {aka long int}
hsp2hitscan.dy:286:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘__time_t’ {aka ‘long int’} [-Wformat=]
  286 |   fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n",
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  287 |           use.ru_utime.tv_sec,
  288 |           use.ru_utime.tv_sec/1000,
      |           ~~~~~~~~~~~~~~~~~~~~~~~~
      |                              |
      |                              __time_t {aka long int}
hsp2hitscan.dy:286:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘__time_t’ {aka ‘long int’} [-Wformat=]
  286 |   fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n",
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
  289 |           use.ru_stime.tv_sec,
      |           ~~~~~~~~~~~~~~~~~~~
      |                       |
      |                       __time_t {aka long int}
hsp2hitscan.dy:286:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘__time_t’ {aka ‘long int’} [-Wformat=]
  286 |   fprintf(stderr,"POPULATION %d.%03du %d.%03ds \n",
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
  290 |           use.ru_stime.tv_sec/1000
      |           ~~~~~~~~~~~~~~~~~~~~~~~~
      |                              |
      |                              __time_t {aka long int}
hsp2hitscan.dy:302:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘__time_t’ {aka ‘long int’} [-Wformat=]
  302 |   fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n",
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  303 |           use.ru_utime.tv_sec,
      |           ~~~~~~~~~~~~~~~~~~~
      |                       |
      |                       __time_t {aka long int}
hsp2hitscan.dy:302:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘__time_t’ {aka ‘long int’} [-Wformat=]
  302 |   fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n",
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  303 |           use.ru_utime.tv_sec,
  304 |           use.ru_utime.tv_sec/1000,
      |           ~~~~~~~~~~~~~~~~~~~~~~~~
      |                              |
      |                              __time_t {aka long int}
hsp2hitscan.dy:302:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘__time_t’ {aka ‘long int’} [-Wformat=]
  302 |   fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n",
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
  305 |           use.ru_stime.tv_sec,
      |           ~~~~~~~~~~~~~~~~~~~
      |                       |
      |                       __time_t {aka long int}
hsp2hitscan.dy:302:18: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘__time_t’ {aka ‘long int’} [-Wformat=]
  302 |   fprintf(stdout,"LINEARISED %d.%03du %d.%03ds \n",
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
  306 |           use.ru_stime.tv_sec/1000
      |           ~~~~~~~~~~~~~~~~~~~~~~~~
      |                              |
      |                              __time_t {aka long int}
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);
      |                           ^
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
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 '/build/reproducible-path/wise-2.4.1/src/dynlibsrc'
(cd external ;  make CC="cc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  `pkg-config --cflags glib-2.0`" all )
make[3]: Entering directory '/build/reproducible-path/wise-2.4.1/src/external'
(cd mott; make CC="cc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread " all)
make[4]: Entering directory '/build/reproducible-path/wise-2.4.1/src/external/mott'
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -Wdate-time -D_FORTIFY_SOURCE=2  -c -o mott_api.o mott_api.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -Wdate-time -D_FORTIFY_SOURCE=2  -c -o gaplib.o gaplib.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../../dynlibsrc -I../../base wise2_mott_bridge.c
ar ru libmott.a mott_api.o gaplib.o wise2_mott_bridge.o
ar: `u' modifier ignored since `D' is the default (see `U')
ar: creating libmott.a
if test -x /bin/ranlib; then /bin/ranlib libmott.a; else exit 0; fi
if test -x /usr/bin/ranlib; then /usr/bin/ranlib libmott.a; else exit 0; fi
make[4]: Leaving directory '/build/reproducible-path/wise-2.4.1/src/external/mott'
make[3]: Leaving directory '/build/reproducible-path/wise-2.4.1/src/external'
(cd socket ; make CC="cc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  `pkg-config --cflags glib-2.0`" libwisesocket.a )
make[3]: Entering directory '/build/reproducible-path/wise-2.4.1/src/socket'
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ functionserver.c
dyc  -l -n Wise2_ -a _api.h -b _api.t -latex -perl functionclient.dy	
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ anonobj.c
Warning Error
	Could not open [methods] for MethodTypeSet reading
Warning Error
	You have no config file called 'methods'. This is bad news for
dynamite matrices. I will attempt to compile, but you cannot use
logical types. 'methods' should be either in the current directory,
the $WISECONFIGDIR or your $WISEPERSONALDIR
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ transferinterface.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ directsocketwrite.c
Warning Error
	You have 3 undocumented functions
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ functionclient.c
functionserver.dy: In function ‘Wise2_main_loop_forking_FunctionServer’:
functionserver.dy:129:11: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  129 |           write(new_socket,buf,9);
      |           ^~~~~~~~~~~~~~~~~~~~~~~
functionserver.dy:141:9: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  141 |         write(new_socket,buf,6);
      |         ^~~~~~~~~~~~~~~~~~~~~~~
functionserver.dy:183:9: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  183 |         write(new_socket,buf,5);
      |         ^~~~~~~~~~~~~~~~~~~~~~~
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 '/build/reproducible-path/wise-2.4.1/src/socket'
(cd dnaindex ; make CC="cc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  `pkg-config --cflags glib-2.0`" all )
make[3]: Entering directory '/build/reproducible-path/wise-2.4.1/src/dnaindex'
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ -I../models kmer_assembly.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ -I../models kmer_index_interface.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ -I../models kmer_direct.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ -I../models kmer_hash.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ -I../models kmer_count.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ -I../models kmer_glib_index.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ -I../models singleseqspace.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ -I../models dnamapping.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ -I../models largeseqreader.c
dyc  -l -n Wise2_ -pthreads -dbtrace 5 -nocwarn kmer_assembly_untangler.dy	
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_contig.c
Warning Error
	Could not open [methods] for MethodTypeSet reading
Warning Error
	You have no config file called 'methods'. This is bad news for
dynamite matrices. I will attempt to compile, but you cannot use
logical types. 'methods' should be either in the current directory,
the $WISECONFIGDIR or your $WISEPERSONALDIR
dyc  -l -n Wise2_ -pthreads -dbtrace 5 -nocwarn kmer_assembly_error.dy	
Warning Error
kmer_assembly_untangler.dy:24:
	For element long - got no good default. Returning 0
Warning Errorcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ -I../models assembly.c

	cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c
Could not open [methods] for MethodTypeSet reading
Warning Error
	You have no config file called 'methods'. This is bad news for
dynamite matrices. I will attempt to compile, but you cannot use
logical types. 'methods' should be either in the current directory,
the $WISECONFIGDIR or your $WISEPERSONALDIR
Warning Error
	You have 14 undocumented functions
Warning Error
	You have 10 undocumented functions
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c
dyc  -l -n Wise2_ -pthreads -dbtrace 5 -nocwarn compressed_protein_index.dy	
Warning Error
	Could not open [methods] for MethodTypeSet reading
Warning Error
	You have no config file called 'methods'. This is bad news for
dynamite matrices. I will attempt to compile, but you cannot use
logical types. 'methods' should be either in the current directory,
the $WISECONFIGDIR or your $WISEPERSONALDIR
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_untangler.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_error.c
Warning Error
	You have 16 undocumented functions
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ -I../models compressed_protein_index.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}
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]);
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
kmer_assembly_error.dy: In function ‘Wise2_mark_tangles_KmerAssembly’:
kmer_assembly_error.dy:93:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=]
   93 |       fprintf(stderr,"Marking node (%ld) [%s] as next tangled\n",node->number,buffer);
      |                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~
      |                                                                      |
      |                                                                      kmer_t {aka long long int}
kmer_assembly_error.dy:105:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=]
  105 |       fprintf(stderr,"Marking node (%ld) [%s] as prev tangled\n",node->number,buffer);
      |                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~
      |                                                                      |
      |                                                                      kmer_t {aka long long int}
kmer_assembly_error.dy: In function ‘Wise2_extend_indel_path_KmerAssembly’:
kmer_assembly_error.dy:351:24: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘int *’ [-Wformat=]
  351 |         fprintf(stderr,"in considering indel (%d, path %d), real (%c) and error (%c) do not agree at position %d,%d\n",delete_length,current_path,real->base,error->base,real_pos,error_pos);
      |                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~               ~~~~~~~~~~~~
      |                                                                                                                                      |
      |                                                                                                                                      int *
kmer_assembly_untangler.dy: In function ‘Wise2_show_KmerAssemblyPath’:
kmer_assembly_untangler.dy:52:65: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
   52 |     fprintf(ofp,"%3d memory %d, from [%s] to [%s], base %c\n",i,(int)kap->stack[i],back,forw,kap->stack[i]->base);
      |                                                                 ^
kmer_assembly_untangler.dy: In function ‘Wise2_untangle_KmerAssembly’:
kmer_assembly_untangler.dy:120:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=]
  120 |       fprintf(stderr,"TANGLE: Node %ld, %s has forward %d and back %d links\n",node->number,buffer,node->next_len,node->prev_len);
      |                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~
      |                                                                                    |
      |                                                                                    kmer_t {aka long long int}
kmer_assembly_untangler.dy:141:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=]
  141 |       fprintf(stderr,"Will attempt untangle starting at %ld to %ld\n",node->prev[i]->prev->number,node->number);
      |                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                                          |
      |                                                                                          kmer_t {aka long long int}
kmer_assembly_untangler.dy:141:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 4 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=]
  141 |       fprintf(stderr,"Will attempt untangle starting at %ld to %ld\n",node->prev[i]->prev->number,node->number);
      |                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                             ~~~~~~~~~~~~
      |                                                                                                       |
      |                                                                                                       kmer_t {aka long long int}
kmer_assembly_untangler.dy:157:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=]
  157 |       fprintf(stderr,"RESOLVED: Node %ld [%s] Fully untangled now...\n",node->number,buffer);
      |                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~
      |                                                                             |
      |                                                                             kmer_t {aka long long int}
kmer_assembly_untangler.dy:159:22: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=]
  159 |       fprintf(stderr,"UNRESOLVED: Node %ld [%s] still tangled...\n",node->number,buffer);
      |                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~
      |                                                                         |
      |                                                                         kmer_t {aka long long int}
kmer_assembly_untangler.dy: In function ‘Wise2_old_attempt_forward_untangle_KmerAssembly’:
kmer_assembly_untangler.dy:444:20: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 3 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=]
  444 |     fprintf(stderr,"looking at node %ld with path length %d, next length %d depth %d\n",current->next->number,pathlen,current->next->next_len,current->sequence_label_len);
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~
      |                                                                                                      |
      |                                                                                                      kmer_t {aka long long int}
kmer_assembly_untangler.dy: In function ‘Wise2_lift_forward_tangled_KmerAssemblyPath’:
kmer_assembly_untangler.dy:753:20: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 6 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=]
  753 |     fprintf(stderr,"Moving stack position %d, depth %d, transfer %d, between %ld [%s] and %ld [%s]\n",i,kap->stack[i]->sequence_label_len,label_len,kap->stack[i]->prev->number,back,kap->stack[i]->next->number,forw);
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                                               ~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                                                                                                                        |
      |                                                                                                                                                                        kmer_t {aka long long int}
kmer_assembly_untangler.dy:753:20: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 8 has type ‘kmer_t’ {aka ‘long long int’} [-Wformat=]
  753 |     fprintf(stderr,"Moving stack position %d, depth %d, transfer %d, between %ld [%s] and %ld [%s]\n",i,kap->stack[i]->sequence_label_len,label_len,kap->stack[i]->prev->number,back,kap->stack[i]->next->number,forw);
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~                                                                                ~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                                                                                                                                                                                                         |
      |                                                                                                                                                                                                         kmer_t {aka long long int}
make[3]: Leaving directory '/build/reproducible-path/wise-2.4.1/src/dnaindex'
(cd network ; make  CC="cc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  `pkg-config --cflags glib-2.0`" all )
make[3]: Entering directory '/build/reproducible-path/wise-2.4.1/src/network'
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/  -I../socket -I../dynlibsrc -I../dnaindex wise_proteinindex_server.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/  -I../socket -I../dynlibsrc -I../dnaindex net_hspscan.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/  -I../socket -I../dynlibsrc -I../dnaindex client_multihspscan.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);
      |                                                                                                       ^~~~~~~~~~~~
cc -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 `pkg-config --libs glib-2.0` -lpthread 
make[3]: Leaving directory '/build/reproducible-path/wise-2.4.1/src/network'
(cd models  ; make CC="cc" CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  `pkg-config --cflags glib-2.0`" EXTRALIBS="-lm" HMMER_DEFINE="HMMER_INTERNAL" HMMER_INCLUDE="../HMMer2/" HMMER_LIBS="../HMMer2/" all )
make[3]: Entering directory '/build/reproducible-path/wise-2.4.1/src/models'
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ dnal.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ dnaalign.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ seqaligndisplay.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ psw.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ proteinsw.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ sw_wrap.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ abc.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ pba.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ pswdb.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ dbac.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ dba.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ slimdba.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ bigdba.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ dbadisplay.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  estwise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I.
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ geneparser21.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ geneparameter.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ genestats.c
dyc  -l -D -n Wise2_ -a _api.h -b _api.t -latex -perl -pthreads -dbtrace 5 -nocwarn genewisehsp.dy	
Warning Error
	Could not open [methods] for MethodTypeSet reading
Warning Error
	You have no config file called 'methods'. This is bad news for
dynamite matrices. I will attempt to compile, but you cannot use
logical types. 'methods' should be either in the current directory,
the $WISECONFIGDIR or your $WISEPERSONALDIR
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ geneutil.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ geneoutput.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ threestatemodel.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ genefrequency.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ splicesitemodeler.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ genewise4.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ genewise6.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ genestretch6.c
Warning Error
	You have not documented new_GeneWiseRunPara_from_argv
Warning Error
	You have not documented show_help_GeneWiseRunPara
Warning Error
	You have not documented DPEnvelope_from_protein_gen
Warning Error
	You have not documented consistent_GeneWiseHSP
Warning Error
	You have not documented compare_GeneWiseHSP_start
Warning Error
	You have not documented add_GeneWiseHSPmanager_HSPset
Warning Error
	You have 6 undocumented functions
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ genewise21.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ geneloop21.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ geneloop6.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ genephase6.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ gwlite.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ gwlitemodel.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ gwrap.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ matchsum.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ estwrap.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ genewisemodel.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ phasemodel.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ cdparser.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ genedisplay.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ estwise3.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ estslim3.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ estloop3.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);
      |                                                                                                       ^~~~~~~~~~~~
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);
      |                                                                                                          ^~~~~~~~~~~~
psw.c: In function ‘show_version’:
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
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);
      |                                                                                                       ^~~~~~~~~~~~
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);
      |                    ^~~~~~~~~~~~~~~~
phasemodel.dy: In function ‘Wise2_read_fasta_PhasedProtein’:
phasemodel.dy:241:3: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  241 |   fgets(name,10000,ifp);
      |   ^~~~~~~~~~~~~~~~~~~~~
phasemodel.dy:241:3: warning: ‘fgets’ writing 10000 bytes into a region of size 2000 overflows the destination [-Wstringop-overflow=]
  241 |   fgets(name,10000,ifp);
      |   ^~~~~~~~~~~~~~~~~~~~~
phasemodel.dy:235:8: note: destination object ‘name’ of size 2000
  235 |   char name[2000];
      |        ^~~~
In file included from /usr/include/stdio.h:970,
                 from ../base/wisebase.h:6,
                 from ../dynlibsrc/probability.h:7,
                 from geneparser21.h:6,
                 from genewisemodel.h:6,
                 from phasemodel.h:6,
                 from phasemodel.c:4:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:305:1: note: in a call to function ‘fgets’ declared with attribute ‘access (write_only, 1, 2)’
  305 | fgets (__fortify_clang_overload_arg (char *, __restrict, __s), int __n,
      | ^~~~~
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ estfrag3.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ estslimloop.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ gwquickdb.c
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);
      |                                                                                                       ^~~~~~~~~~~~
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ threestatedb.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ pfamhmmer1db.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ pwmdna.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../HMMer2/ -DHMMER_INTERNAL -I../base/ -I../dynlibsrc/ wise2xhmmer2.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ genewisemodeldb.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ seqhit.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ standardout.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ geneparser4.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ estquick3.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  genewise.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I.
In function ‘fgets’,
    inlined from ‘Wise2_read_fasta_PhasedProtein’ at phasemodel.dy:241:3:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning]
  316 |     return __fgets_chk_warn (__s, __sz, __n, __stream);
      |            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  genewisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ 
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  estwisedb.c -I../base/ -I../dynlibsrc/ -I../HMMer2/
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ genomewise.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ genomewise9.c
genomewise.c: In function ‘show_version’:
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ genome_evidence.c
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);
      |                                                                                                       ^~~~~~~~~~~~
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);
      |                                                                                                       ^~~~~~~~~~~~
dyc  -l -D -n Wise2_ -a _api.h -b _api.t -latex -perl -pthreads -dbtrace 5 -nocwarn est_evidence.dy	
Warning Error
	Could not open [methods] for MethodTypeSet reading
Warning Error
	You have no config file called 'methods'. This is bad news for
dynamite matrices. I will attempt to compile, but you cannot use
logical types. 'methods' should be either in the current directory,
the $WISECONFIGDIR or your $WISEPERSONALDIR
Warning Error
	You have not documented indicate_intron_used
Warning Error
	You have not documented read_est_evidence
Warning Error
	You have not documented new_est_GenomeEvidenceUnit
Warning Error
	You have not documented est_utr5_start
Warning Error
	You have not documented est_utr3_end
Warning Error
	You have not documented est_start_pot
Warning Error
	You have not documented est_stop_pot
Warning Error
	You have not documented est_cds_frameshift
Warning Error
	You have not documented est_cds_3SS
Warning Error
	You have not documented est_cds_5SS
Warning Error
	You have not documented est_intron_pot
Warning Error
	You have not documented est_cds_pot
Warning Error
	You have not documented est_3ss
Warning Error
	You have not documented est_5ss
Warning Error
	You have not documented est_utr_pot
Warning Error
	You have 15 undocumented functions
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ sywise.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ sywise20.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ syexonmodel.c
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);
      |                                                                                                       ^~~~~~~~~~~~
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ pseudowise.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ pseudowise7.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` promoterwise.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ localdba.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` localcishit.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);
      |                                                                                                       ^~~~~~~~~~~~
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);
      |                                                                                                       ^~~~~~~~~~~~
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ localcispara.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ motifmatrix.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ motifmatrixdp.c
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);
      |                                                                                                       ^~~~~~~~~~~~
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ transfactor.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ pairwiseshortdna.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++)  {
      |                        ^
cc  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/  -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.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);
      |                                                                                                       ^~~~~~~~~~~~
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` hsp2aln_sw.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ genewisehsp.c
cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/wise-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wno-error=int-conversion -Wdate-time -D_FORTIFY_SOURCE=2 -c  -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/sysprof-6 -pthread  -I../base/ -I../dynlibsrc/ est_evidence.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);
      |                                                                                                       ^~~~~~~~~~~~
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/include/stdio.h:970,
                 from ../base/wisebase.h:6,
                 from pwmdna.h:6,
                 from transfactor.h:6,
                 from transfactor.c:4:
In function ‘sprintf’,
    inlined from ‘Wise2_read_ben_IUPAC_TransFactorSet’ at transfactor.dy:680:5:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 9 and 529 bytes into a destination of size 512
   30 |   return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   31 |                                   __glibc_objsize (__s), __fmt,
      |                                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   32 |                                   __va_arg_pack ());
      |                                   ~~~~~~~~~~~~~~~~~
cc -o dnal dnal.o dnaalign.o seqaligndisplay.o -Wl,-z,relro -Wl,-z,now -L../base/ -L../dynlibsrc/ -L../HMMer2/ -lpthread `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm
cc -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 `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm
cc -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 `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm
cc -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 `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 `pkg-config --libs glib-2.0`
cc -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 `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm `pkg-config --libs glib-2.0` -lpthread
cc -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 `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm
cc -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 `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm
cc -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 `pkg-config --libs glib-2.0` -ldyna_glib -ldyna -lwisebase  -lm
cc -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 `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 `pkg-config --libs glib-2.0`
cc -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 `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 `pkg-config --libs glib-2.0`
cc -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 `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 `pkg-config --libs glib-2.0`
cc -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 `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 `pkg-config --libs glib-2.0`
cc -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 `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 `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 '/build/reproducible-path/wise-2.4.1/src/models'
make bin
make[3]: Entering directory '/build/reproducible-path/wise-2.4.1/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 /build/reproducible-path/wise-2.4.1/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 '/build/reproducible-path/wise-2.4.1/src'
make[2]: Leaving directory '/build/reproducible-path/wise-2.4.1/src'
/usr/bin/make -C debian/manpages.d
make[2]: Entering directory '/build/reproducible-path/wise-2.4.1/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 '/build/reproducible-path/wise-2.4.1/debian/manpages.d'
find src/models/ src/dynlibsrc/ -name '*.tex' -print0 | LC_ALL=C sort -z | xargs -0 cat | perl docs/gettex.pl > docs/temp.tex
cat docs/wise2api.tex docs/temp.tex docs/apiend.tex > docs/api.tex
sed -i 's/ sw_wrap / sw\\_wrap /' docs/api.tex
sed -i 's/label{module_sequence\\_codon}/label{module_sequence_codon}/' docs/api.tex
sed -i 's/Wise2::GeneParameter21_wrap/Wise2::GeneParameter21\\_wrap/' docs/api.tex
cd docs && pdflatex api.tex
This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./api.tex
LaTeX2e <2024-11-01> patch level 2
L3 programming layer <2025-01-18>
(/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 2024/06/29 v1.4n Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))
(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def)
No file api.aux.
(/usr/share/texlive/texmf-dist/tex/latex/base/ulasy.fd)
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}]
No file api.toc.

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[]    \OT1/cmtt/m/n/10 print "You must give a file to revcom for a reverse to w
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[]\OT1/cmr/m/n/10 Build an en-tire pa-ram-e-ter set for ge-newise us-ing Wise2:
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[42]

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[43]

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ine 2298.


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[44]
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[]\OT1/cmtt/m/n/10 &Wise2::GenomicRegion::read[]EMBL[]GenomicRegion[]file (file
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[45]
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[48]

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[]   \OT1/cmtt/m/n/10 b) cooperation with future versions of histogram.c would 
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[49]
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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
,wonka,ndegrees) 

[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
,double in-ter-nal[]score[]level)

[55]
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[59]

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e 3231.


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[60]

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[61]
[62]

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

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[64]

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e 3592.


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[65]

LaTeX Warning: Reference `object_RandomModelDNA' on page 66 undefined on input 
line 3642.


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e 3644.


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[66]

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LaTeX Warning: Reference `object_Sequence' on page 67 undefined on input line 3
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e 3715.


[67]

LaTeX Warning: Reference `accessing_fields' on page 68 undefined on input line 
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[68]
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[]\OT1/cmtt/m/n/10 Wise2[]force[]to[]dna[]Sequence (seq,fraction,number[]of[]co
nver) 

[69]
[70]
[71]
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[73]
[74]

LaTeX Warning: Reference `accessing_fields' on page 75 undefined on input line 
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[75]
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[77]

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



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

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LaTeX Warning: Reference `accessing_fields' on page 79 undefined on input line 
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[79]

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


LaTeX Warning: Reference `accessing_fields' on page 80 undefined on input line 
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Overfull \hbox (24.01358pt too wide) in paragraph at lines 4508--4515
\OT1/cmr/m/n/10 have any se-quence in it. When se-quence is asked for by get[]P
rotein[]from[]Translation()

[80]

LaTeX Warning: Reference `object_cDNAParser' on page 81 undefined on input line
 4549.


[81]

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LaTeX Warning: Reference `object_DnaStartEnd' on page 82 undefined on input lin
e 4602.


Overfull \hbox (62.7533pt too wide) in paragraph at lines 4609--4610
[]\OT1/cmtt/m/n/10 Wise2[]make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap,
text,dpri) 

Overfull \hbox (40.0498pt too wide) in paragraph at lines 4610--4611
[]\OT1/cmtt/m/n/10 &Wise2::make[]align[]dnaalign (one,two,mat,se,qgap,qext,tgap
,text,dpri) 

[82]

LaTeX Warning: Reference `accessing_fields' on page 83 undefined on input line 
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Overfull \hbox (335.96082pt too wide) in paragraph at lines 4671--4672
[]\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]TSM[]estwise (tdb,cdb,cp,cm,rmd,use[]sy
n,alg,bits[]cutoff,allN,flat[]insert,report[]level,die[]on[]error,dbsi) 

Overfull \hbox (313.25732pt too wide) in paragraph at lines 4672--4673
[]\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]TSM[]estwise (tdb,cdb,cp,cm,rmd,use[]s
yn,alg,bits[]cutoff,allN,flat[]insert,report[]level,die[]on[]error,dbsi) 

[83]
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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,
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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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Overfull \hbox (205.94829pt too wide) in paragraph at lines 4733--4734
[]\OT1/cmtt/m/n/10 &Wise2::AlnBlock[]from[]TSM[]estwise[]wrap (tsm,cdna,cp,cm,c
t,rmd,alg,use[]syn,force[]flat[]insert,allN,dpri) 

[85]
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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) 

[86]
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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) 

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
ine 4832.


LaTeX Warning: Reference `object_GeneSingleCons' on page 87 undefined on input 
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[87]

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Overfull \hbox (1.40793pt too wide) in paragraph at lines 4893--4894
[]\OT1/cmr/m/n/10 transition[GENEFREQUENCY21[]TRANSITION[]LEN] Type [dou-ble : 
Scalar]

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

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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
ne 4992.


LaTeX Warning: Reference `accessing_fields' on page 90 undefined on input line 
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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) 

[90]
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[]\OT1/cmtt/m/n/10 Wise2[]MatchSummarySet[]from[]AlnBlock[]genewise (alb,qname,
protoff,target) 

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

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[]\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->MatchSummarySet[]from[]AlnBlock[]gene
wise(qname,protoff,target) 

LaTeX Warning: Reference `accessing_fields' on page 91 undefined on input line 
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[91]

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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
et,name,main,ofp) 

Overfull \hbox (70.07953pt too wide) in paragraph at lines 5175--5176
[]\OT1/cmtt/m/n/10 &Wise2::write[]pretty[]str[]align (alb,qname,query,tname,tar
get,name,main,ofp) 

[93]
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[]\OT1/cmtt/m/n/10 Wise2[]write[]pretty[]Protein[]align (alb,q,t,name,main,ofp)
 

LaTeX Warning: Reference `object_DnaSequenceHitList' on page 94 undefined on in
put line 5243.


LaTeX Warning: Reference `object_SegmentHitList' on page 94 undefined on input 
line 5245.


LaTeX Warning: Reference `object_SegmentHit' on page 94 undefined on input line
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[94]

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[]\OT1/cmtt/m/n/10 &Wise2::DnaSequenceHitList::read[]MSPcrunch[]DnaSequenceHitL
ist (ifp) 

[95]

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

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

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[]\OT1/cmtt/m/n/10 &Wise2::Align[]Sequences[]ProteinSmithWaterman (one,two,comp
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[]\OT1/cmr/m/n/10 [OWNER] new AlnBlock struc-ture rep-re-sent-ing the align-men
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[97]
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[98]
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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
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[]\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinSW (querydb,targetdb,comp,gap,e
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[99]
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[]\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b,c
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[]\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinABC (querydb,targetdb,comp,a,b,
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[100]
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[]\OT1/cmtt/m/n/10 Wise2[]Hscore[]from[]ProteinBA (querydb,targetdb,comp,bentry
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[]\OT1/cmtt/m/n/10 &Wise2::Hscore[]from[]ProteinBA (querydb,targetdb,comp,bentr
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LaTeX Warning: Reference `object_ThreeStateDB' on page 101 undefined on input l
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[101]
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[]\OT1/cmr/m/n/10 reload[]generic Type [Three-State-Model * (*reload[]generic)(
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[]\OT1/cmr/m/n/10 dataentry[]add Type [boolean (*dataen-try[]add)(ThreeStateDB 
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[]\OT1/cmr/m/n/10 index[]generic Type [Three-State-Model * (*in-dex[]generic)(T
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[103]
[104]

LaTeX Warning: Reference `object_ThreeStateModel' on page 105 undefined on inpu
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LaTeX Warning: Reference `object_ThreeStateUnit' on page 105 undefined on input
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LaTeX Warning: Reference `accessing_fields' on page 105 undefined on input line
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[105]
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[]\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->force[]weighted[]local[]model(prob[]i
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[106]
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[]\TS1/cmtt/m/n/10 $\OT1/cmtt/m/n/10 obj->ThreeStateModel[]from[]half[]bit[]Seq
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[]\OT1/cmtt/m/n/10 &Wise2::ThreeStateModel::write[]HMMer[]1[]7[]ascii[]ThreeSta
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LaTeX Warning: Reference `accessing_fields' on page 107 undefined on input line
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[107]
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cd docs && pdflatex api.tex
This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./api.tex
LaTeX2e <2024-11-01> patch level 2
L3 programming layer <2025-01-18>
(/usr/share/texlive/texmf-dist/tex/latex/base/latex209.def

          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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[]    \OT1/cmtt/m/n/10 print "You must give a file to revcom for a reverse to w
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[]\OT1/cmr/m/n/10 Build an en-tire pa-ram-e-ter set for ge-newise us-ing Wise2:
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\OT1/cmr/m/n/10 AlnBlock is the main rep-re-sen-ta-tion of align-ments from Dy-
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[]\OT1/cmtt/m/n/10 &Wise2::CodonMapper::sprinkle[]errors[]over[]CodonMapper (cm
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[]\OT1/cmtt/m/n/10 Wise2[]Genomic[]from[]Sequence[]Nheuristic (seq,length[]of[]
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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 (seqdb,cses,length[]of[]N,repeat[]in[]
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[]   \OT1/cmtt/m/n/10 b) cooperation with future versions of histogram.c would 
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[]\OT1/cmtt/m/n/10 Wise2[]ExtremeValueSetHistogram (h,mu,lambda,lowbound,highbo
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[]\OT1/cmtt/m/n/10 Wise2[]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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[]\OT1/cmtt/m/n/10 Wise2[]AlnBlock[]from[]Protein[]estwise[]wrap (pro,cdna,cp,c
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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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Transcript written on api.log.
cd docs && pdflatex dynamite.tex
This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./dynamite.tex
LaTeX2e <2024-11-01> patch level 2
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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[] 

Overfull \hbox (17.24684pt too wide) in paragraph at lines 588--588
[]   \OT1/cmtt/m/n/10 * -e for ext value (an int) - rely on commandline error p
rocessing[] 

[11]
Overfull \hbox (269.24464pt too wide) in paragraph at lines 588--588
[]  \OT1/cmtt/m/n/10 if( strip_out_boolean_argument(&argc,argv,"h") == TRUE || 
strip_out_boolean_argument(&argc,argv,"-help") == TRUE) {[] 

Overfull \hbox (43.49661pt too wide) in paragraph at lines 588--588
[]    \OT1/cmtt/m/n/10 warn("Must have two arguments for sequence 1 and sequenc
e 2 %d",argc);[] 

[12]
Overfull \hbox (22.4968pt too wide) in paragraph at lines 588--588
[]   \OT1/cmtt/m/n/10 * or WISEPERSONALDIR if it is not present in the current 
directory.[] 

Overfull \hbox (48.74657pt too wide) in paragraph at lines 588--588
[]    \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s
",query->name);[] 

Overfull \hbox (53.99652pt too wide) in paragraph at lines 588--588
[]    \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s
",target->name);[] 

Overfull \hbox (43.49661pt too wide) in paragraph at lines 588--588
[]   \OT1/cmtt/m/n/10 * If the sequences are small enough then it should use ex
plicit memory.[] 

[13]
Overfull \hbox (59.24648pt too wide) in paragraph at lines 588--588
[]  \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp
,-gap,-ext,NULL);[] 

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

[14]
Overfull \hbox (48.74657pt too wide) in paragraph at lines 632--632
[]    \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s
",query->name);[] 

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

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

Overfull \hbox (59.24648pt too wide) in paragraph at lines 632--632
[]  \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp
,-gap,-ext,NULL);[] 

[15]
Overfull \hbox (80.24629pt too wide) in paragraph at lines 632--632
[]    \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query
->name,target->name);[] 

Overfull \hbox (32.9967pt too wide) in paragraph at lines 639--639
[]  \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp
,-gap,-ext);[] 

Overfull \hbox (48.74657pt too wide) in paragraph at lines 654--654
[]    \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s
",query->name);[] 

[16]
Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738
[]\OT1/cmtt/m/n/10 Q22037               EPENLRKIFVGGLTSNTTDDLMREFYSQFGEITDIIVMR
DPTTKRSRGF[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738
[]                     \OT1/cmtt/m/n/10 EPE LRK+F+GGL+  TTD+ +R  + Q+G +TD +VMR
DP TKRSRGF[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738
[]\OT1/cmtt/m/n/10 ROA1_HUMAN           EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMR
DPNTKRSRGF[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738
[]\OT1/cmtt/m/n/10 Q22037               GFVTFSGKTEVDAAMKQRPHIIDGKTVDPKRAVPRDDKN
RSESNVSTKR[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738
[]                     \OT1/cmtt/m/n/10 GFVT++   EVDAAM  RPH +DG+ V+PKRAV R+D  
R  ++++ K+[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738
[]\OT1/cmtt/m/n/10 ROA1_HUMAN           GFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQ
RPGAHLTVKK[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738
[]\OT1/cmtt/m/n/10 Q22037               LYVSGVREDHTEDMLTEYFTKYGTVTKSEIILDKATQKP
RGFGFVTFDD[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738
[]                     \OT1/cmtt/m/n/10 ++V G++ED  E  L +YF +YG +   EI+ D+ + K 
RGF FVTFDD[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738
[]\OT1/cmtt/m/n/10 ROA1_HUMAN           IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKK
RGFAFVTFDD[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738
[]\OT1/cmtt/m/n/10 Q22037               HDSVDQCVLQKSHMVNGHRCDVRKGLSKDEMSKAQMNRD
RETRGGRSRD[] 

Overfull \hbox (11.99689pt too wide) in paragraph at lines 738--738
[]                     \OT1/cmtt/m/n/10 HDSVD+ V+QK H VNGH C+VRK LSK EM+ A     
  ++ GRS[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738
[]\OT1/cmtt/m/n/10 ROA1_HUMAN           HDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASAS----
-SSQRGRSGS[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738
[]\OT1/cmtt/m/n/10 Q22037               GQRGGYNGGG-GGGGGWGGPAQRGGPGAYGGP-GGGGQG
GYGGDYGG--[] 

Overfull \hbox (11.99689pt too wide) in paragraph at lines 738--738
[]                     \OT1/cmtt/m/n/10 G  GG  GGG GG   +G      G G +GG  GGGG G
G G  Y G[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738
[]\OT1/cmtt/m/n/10 ROA1_HUMAN           GNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSRGGGGYG
GSGDGYNGFG[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738
[]\OT1/cmtt/m/n/10 Q22037               GWGQQGGGGQGGWGGPQQQQGGG-GWGQQGGGGQGGWGG
PQQQQQGGWG[] 

Overfull \hbox (11.99689pt too wide) in paragraph at lines 738--738
[]                       \OT1/cmtt/m/n/10 G  GGGG G  GG +    GG G+G QG G  GG G 
      GG[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738
[]\OT1/cmtt/m/n/10 ROA1_HUMAN           NDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSG-YGGSGS
YDSYNNGGGR[] 

[17]
[18]
Overfull \hbox (48.88945pt too wide) in paragraph at lines 793--795
[]\OT1/cmr/m/n/10 The align-ment is the set of (i,j,<state>) triples, where sta
te is one of (Match,Insert,Delete)

[19]
[20]
Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942
[]          \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta
rget,j))"[] 

[21]
Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942
[]          \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta
rget,j))"[] 

Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942
[]          \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta
rget,j))"[] 

Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942
[]          \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta
rget,j))"[] 

[22]
Overfull \hbox (32.64503pt too wide) in paragraph at lines 1015--1019
\OT1/cmr/m/n/10 and GE-NOMIC[]INTRON. No-tice how the source lines to and from 
GE-NOMIC[]INSERT

Overfull \hbox (38.24666pt too wide) in paragraph at lines 1116--1116
[]\OT1/cmtt/m/n/10 #define DnaMatrix_Score(dnamat,base1,base2) (dnamat->score[b
ase1][base2])[] 

[23]
Overfull \hbox (11.99689pt too wide) in paragraph at lines 1116--1116
[]  \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,i),GENOMIC_BASE(tar
get,j))"[] 

[24]
[25]
Overfull \hbox (122.24593pt too wide) in paragraph at lines 1335--1335
[]  \OT1/cmtt/m/n/10 fprintf(ofp,"\nest2gen <options> est-seq genomic-seq\nBoth
 sequences in fasta format\n"[] 

[26]
Overfull \hbox (269.24464pt too wide) in paragraph at lines 1335--1335
[]  \OT1/cmtt/m/n/10 if( strip_out_boolean_argument(&argc,argv,"h") == TRUE || 
strip_out_boolean_argument(&argc,argv,"-help") == TRUE) {[] 

[27]
Overfull \hbox (43.49661pt too wide) in paragraph at lines 1335--1335
[]    \OT1/cmtt/m/n/10 warn("Must have two arguments for sequence 1 and sequenc
e 2 %d",argc);[] 

Overfull \hbox (27.74675pt too wide) in paragraph at lines 1335--1335
[]   \OT1/cmtt/m/n/10 * To do this we need a cdna ComplexSequenceEvalSet and a 
genomic one[] 

Overfull \hbox (53.99652pt too wide) in paragraph at lines 1335--1335
[]   \OT1/cmtt/m/n/10 * Really our genomic model should be alot more complex. T
he 'default' one[] 

Overfull \hbox (38.24666pt too wide) in paragraph at lines 1335--1335
[]   \OT1/cmtt/m/n/10 * has 0 at GT----AG for 5' and 3' splice sites, and NEGI 
(= -infinity)[] 

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

Overfull \hbox (43.49661pt too wide) in paragraph at lines 1335--1335
[]   \OT1/cmtt/m/n/10 * other machinery, but not for now <grin>. See the genewi
se code if you[] 

[28]
Overfull \hbox (48.74657pt too wide) in paragraph at lines 1335--1335
[]    \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s
",query->name);[] 

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

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

Overfull \hbox (43.49661pt too wide) in paragraph at lines 1335--1335
[]   \OT1/cmtt/m/n/10 * program. Firstly we are treating errors similarly on ea
ch side of the[] 

Overfull \hbox (59.24648pt too wide) in paragraph at lines 1335--1335
[]   \OT1/cmtt/m/n/10 * Secondly there is a rather complex interaction between 
the gap/extension[] 

Overfull \hbox (53.99652pt too wide) in paragraph at lines 1335--1335
[]   \OT1/cmtt/m/n/10 * of what is thought to be sequencing error and the intro
ns. Here we have[] 

Overfull \hbox (64.49643pt too wide) in paragraph at lines 1335--1335
[]   \OT1/cmtt/m/n/10 * one more parameter, and intron open penalty, which can 
be set, to prevent[] 

Overfull \hbox (48.74657pt too wide) in paragraph at lines 1335--1335
[]   \OT1/cmtt/m/n/10 * One good way to parameterise all this would be to have 
a probabilistic[] 

Overfull \hbox (48.74657pt too wide) in paragraph at lines 1335--1335
[]   \OT1/cmtt/m/n/10 * model of the processes, derive probabilities and then m
ap them to ints[] 

Overfull \hbox (27.74675pt too wide) in paragraph at lines 1335--1335
[]   \OT1/cmtt/m/n/10 * (probability.h has got these mappings, such as Probabil
ity2Score).[] 

Overfull \hbox (101.24611pt too wide) in paragraph at lines 1335--1335
[]  \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_cDNA2Gen(query_cs,target_cs,dm,ga
p,-ext,-gap,-ext,0,NULL);[] 

Overfull \hbox (80.24629pt too wide) in paragraph at lines 1335--1335
[]    \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query
->name,target->name);[] 

[29]
Overfull \hbox (74.99634pt too wide) in paragraph at lines 1342--1342
[]  \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_cDNA2Gen(query_cs,target_cs,dm,ga
p,-ext,-gap,-ext,0);[] 

[30]
Overfull \hbox (27.74675pt too wide) in paragraph at lines 1379--1379
[]   \OT1/cmtt/m/n/10 * To do this we need a cdna ComplexSequenceEvalSet and a 
genomic one[] 

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]\OT1/cmtt/m/n/10 HSHNRNPA        3959 AAG<-3962:4251->GTGGCTATGGCGGTTCCAGCAGC
AGCAGTAGCT[] 

[33]
Overfull \hbox (22.4968pt too wide) in paragraph at lines 1572--1572
[]\OT1/cmtt/m/n/10 query  type="MySequence*"  name="query" field:len="length_of
_sequence"[] 

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

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

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

Overfull \hbox (127.49588pt too wide) in paragraph at lines 1634--1634
[]      \OT1/cmtt/m/n/10 fprintf(stdout,"%d,%d are matched with score %d\n",uni
t->i+1,unit->j+1,unit->score);[] 

[36]
Overfull \hbox (22.4968pt too wide) in paragraph at lines 1727--1727
[]\OT1/cmtt/m/n/10 query  type="MySequence*"  name="query" field:len="length_of
_sequence"[] 

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

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

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

[39]
Overfull \hbox (258.74474pt too wide) in paragraph at lines 1849--1849
[]  \OT1/cmtt/m/n/10 calc="ALPHA_SEQ_SCORE(query,i) + ALPHA_SEQ_SCORE(target,j)
 + mat_alpha.comp[SEQ_POS(query,i)][SEQ_POS(target,j)]"[] 

[40]
[41]
Overfull \hbox (20.54509pt too wide) in paragraph at lines 1911--1912
[]\OT1/cmr/m/n/10 The macro Dna-Ma-trix[]Score which is de-fined at the top of 
the cdna2genomic.dy

Overfull \hbox (17.24684pt too wide) in paragraph at lines 1928--1928
[]  \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,i),GENOMIC_CODON(ta
rget,j))"[] 

[42]
Overfull \hbox (53.99652pt too wide) in paragraph at lines 1944--1944
[]        \OT1/cmtt/m/n/10 Mis-type in argument 3 of DNA\_MAT\_SCORE: wanted [b
ase] got [codon][] 

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

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

Overfull \hbox (11.99689pt too wide) in paragraph at lines 1967--1967
[]\OT1/cmtt/m/n/10 expect to paired directly in a function. This is just a warn
ing that[] 

[43]
Overfull \hbox (17.24684pt too wide) in paragraph at lines 2014--2014
[]  \OT1/cmtt/m/n/10 throw_warning("Letter %c does not exist in comparison matr
ix",one);[] 

Overfull \hbox (17.24684pt too wide) in paragraph at lines 2014--2014
[]  \OT1/cmtt/m/n/10 throw_warning("Letter %c does not exist in comparison matr
ix",two);[] 

[44]
[45]
Overfull \hbox (74.99634pt too wide) in paragraph at lines 2255--2255
[]  \OT1/cmtt/m/n/10 fprintf(stdout,"dbsearch [options] <protein-seq> <protein-
fasta-database>\n");[] 

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

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

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

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

Overfull \hbox (53.99652pt too wide) in paragraph at lines 2255--2255
[]      \OT1/cmtt/m/n/10 is not too likely, and this makes this program future 
proof wrt to new[] 

[46]
Overfull \hbox (43.49661pt too wide) in paragraph at lines 2255--2255
[]   \OT1/cmtt/m/n/10 * care about which implementation is used, and does not k
now either (!)[] 

[47]
Overfull \hbox (106.49606pt too wide) in paragraph at lines 2255--2255
[]  \OT1/cmtt/m/n/10 /* 10 means a score cutoff of 10, -1 means don't report on
 stderr search progress */[] 

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

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

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

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

Overfull \hbox (1.49698pt too wide) in paragraph at lines 2255--2255
[]      \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta
rget);[] 

[48]
Overfull \hbox (74.99634pt too wide) in paragraph at lines 2255--2255
[] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s",t
emp->baseseq->name);[] 

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

Overfull \hbox (101.24611pt too wide) in paragraph at lines 2255--2255
[] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query->n
ame,temp->baseseq->name);[] 

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

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

Overfull \hbox (53.99652pt too wide) in paragraph at lines 2263--2263
[]    \OT1/cmtt/m/n/10 fatal("Some sort of error in the database search. Dieing
 ungracefully");[] 

[49]
Overfull \hbox (1.49698pt too wide) in paragraph at lines 2292--2292
[]      \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta
rget);[] 

[50]
[51]
[52]
[53]
[54]
Overfull \hbox (1.32472pt too wide) in paragraph at lines 2528--2534
\OT1/cmr/m/n/10 de-scribed by a "state...endstate" multi-line block. Within eac
h "state...endstate"

[55]
[56]
[57]
[58]
[59]
Overfull \hbox (1.75064pt too wide) in paragraph at lines 2772--2776
\OT1/cmr/m/n/10 Dy-na-mite file: for ex-am-ple the fol-low-ing er-ror was made 
by mistyp-ing ``MATCH''

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

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

[60]
[61]
[62] (./dynamite.aux)

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knappen/ec/tcrm1000.600pk></usr/share/texlive/texmf-dist/fonts/type1/public/ams
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exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive
/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb>
Output written on dynamite.pdf (62 pages, 221240 bytes).
Transcript written on dynamite.log.
cd docs && pdflatex dynamite.tex
This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./dynamite.tex
LaTeX2e <2024-11-01> patch level 2
L3 programming layer <2025-01-18>
(/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 2024/06/29 v1.4n Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))
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(./dynamite.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ulasy.fd)
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./dynamite.toc
[2]
Overfull \hbox (8.02837pt too wide) in paragraph at lines 50--50
 [][] []\OT1/cmr/m/n/10 [Dynamite Level] Did not un-der-stand line [ source MAT
CH]. 
)
[3]
[4]
[5]
[6]
[7]
[8]
Overfull \hbox (4.11092pt too wide) in paragraph at lines 253--257
\OT1/cmr/m/n/10 tri-bu-tion from 'ftp://ftp.sanger.ac.uk/pub/birney/dynamite/dy
n.x.tar.Z' (where

[9]
[10]
[11]
[12]
Overfull \hbox (48.74657pt too wide) in paragraph at lines 588--588
[]  \OT1/cmtt/m/n/10 fprintf(ofp,"\npsw <options> seq1 seq2\nBoth sequences in 
fasta format\n"[] 

Overfull \hbox (17.24684pt too wide) in paragraph at lines 588--588
[]   \OT1/cmtt/m/n/10 * -g for gap value (an int) - rely on commandline error p
rocessing[] 

Overfull \hbox (17.24684pt too wide) in paragraph at lines 588--588
[]   \OT1/cmtt/m/n/10 * -e for ext value (an int) - rely on commandline error p
rocessing[] 

[13]
Overfull \hbox (269.24464pt too wide) in paragraph at lines 588--588
[]  \OT1/cmtt/m/n/10 if( strip_out_boolean_argument(&argc,argv,"h") == TRUE || 
strip_out_boolean_argument(&argc,argv,"-help") == TRUE) {[] 

Overfull \hbox (43.49661pt too wide) in paragraph at lines 588--588
[]    \OT1/cmtt/m/n/10 warn("Must have two arguments for sequence 1 and sequenc
e 2 %d",argc);[] 

[14]
Overfull \hbox (22.4968pt too wide) in paragraph at lines 588--588
[]   \OT1/cmtt/m/n/10 * or WISEPERSONALDIR if it is not present in the current 
directory.[] 

Overfull \hbox (48.74657pt too wide) in paragraph at lines 588--588
[]    \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s
",query->name);[] 

Overfull \hbox (53.99652pt too wide) in paragraph at lines 588--588
[]    \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s
",target->name);[] 

Overfull \hbox (43.49661pt too wide) in paragraph at lines 588--588
[]   \OT1/cmtt/m/n/10 * If the sequences are small enough then it should use ex
plicit memory.[] 

[15]
Overfull \hbox (59.24648pt too wide) in paragraph at lines 588--588
[]  \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp
,-gap,-ext,NULL);[] 

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

[16]
Overfull \hbox (48.74657pt too wide) in paragraph at lines 632--632
[]    \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s
",query->name);[] 

Overfull \hbox (53.99652pt too wide) in paragraph at lines 632--632
[]    \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s
",target->name);[] 

Overfull \hbox (43.49661pt too wide) in paragraph at lines 632--632
[]   \OT1/cmtt/m/n/10 * If the sequences are small enough then it should use ex
plicit memory.[] 

Overfull \hbox (59.24648pt too wide) in paragraph at lines 632--632
[]  \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp
,-gap,-ext,NULL);[] 

[17]
Overfull \hbox (80.24629pt too wide) in paragraph at lines 632--632
[]    \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query
->name,target->name);[] 

Overfull \hbox (32.9967pt too wide) in paragraph at lines 639--639
[]  \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_ProteinSW(query_cs,target_cs,comp
,-gap,-ext);[] 

Overfull \hbox (48.74657pt too wide) in paragraph at lines 654--654
[]    \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s
",query->name);[] 

[18]
Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738
[]\OT1/cmtt/m/n/10 Q22037               EPENLRKIFVGGLTSNTTDDLMREFYSQFGEITDIIVMR
DPTTKRSRGF[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738
[]                     \OT1/cmtt/m/n/10 EPE LRK+F+GGL+  TTD+ +R  + Q+G +TD +VMR
DP TKRSRGF[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738
[]\OT1/cmtt/m/n/10 ROA1_HUMAN           EPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMR
DPNTKRSRGF[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738
[]\OT1/cmtt/m/n/10 Q22037               GFVTFSGKTEVDAAMKQRPHIIDGKTVDPKRAVPRDDKN
RSESNVSTKR[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738
[]                     \OT1/cmtt/m/n/10 GFVT++   EVDAAM  RPH +DG+ V+PKRAV R+D  
R  ++++ K+[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738
[]\OT1/cmtt/m/n/10 ROA1_HUMAN           GFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQ
RPGAHLTVKK[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738
[]\OT1/cmtt/m/n/10 Q22037               LYVSGVREDHTEDMLTEYFTKYGTVTKSEIILDKATQKP
RGFGFVTFDD[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738
[]                     \OT1/cmtt/m/n/10 ++V G++ED  E  L +YF +YG +   EI+ D+ + K 
RGF FVTFDD[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738
[]\OT1/cmtt/m/n/10 ROA1_HUMAN           IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKK
RGFAFVTFDD[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738
[]\OT1/cmtt/m/n/10 Q22037               HDSVDQCVLQKSHMVNGHRCDVRKGLSKDEMSKAQMNRD
RETRGGRSRD[] 

Overfull \hbox (11.99689pt too wide) in paragraph at lines 738--738
[]                     \OT1/cmtt/m/n/10 HDSVD+ V+QK H VNGH C+VRK LSK EM+ A     
  ++ GRS[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738
[]\OT1/cmtt/m/n/10 ROA1_HUMAN           HDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASAS----
-SSQRGRSGS[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738
[]\OT1/cmtt/m/n/10 Q22037               GQRGGYNGGG-GGGGGWGGPAQRGGPGAYGGP-GGGGQG
GYGGDYGG--[] 

Overfull \hbox (11.99689pt too wide) in paragraph at lines 738--738
[]                     \OT1/cmtt/m/n/10 G  GG  GGG GG   +G      G G +GG  GGGG G
G G  Y G[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738
[]\OT1/cmtt/m/n/10 ROA1_HUMAN           GNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSRGGGGYG
GSGDGYNGFG[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738
[]\OT1/cmtt/m/n/10 Q22037               GWGQQGGGGQGGWGGPQQQQGGG-GWGQQGGGGQGGWGG
PQQQQQGGWG[] 

Overfull \hbox (11.99689pt too wide) in paragraph at lines 738--738
[]                       \OT1/cmtt/m/n/10 G  GGGG G  GG +    GG G+G QG G  GG G 
      GG[] 

Overfull \hbox (22.4968pt too wide) in paragraph at lines 738--738
[]\OT1/cmtt/m/n/10 ROA1_HUMAN           NDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSG-YGGSGS
YDSYNNGGGR[] 

[19]
[20]
Overfull \hbox (48.88945pt too wide) in paragraph at lines 793--795
[]\OT1/cmr/m/n/10 The align-ment is the set of (i,j,<state>) triples, where sta
te is one of (Match,Insert,Delete)

[21]
[22]
Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942
[]          \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta
rget,j))"[] 

[23]
Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942
[]          \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta
rget,j))"[] 

Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942
[]          \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta
rget,j))"[] 

Overfull \hbox (17.24684pt too wide) in paragraph at lines 942--942
[]          \OT1/cmtt/m/n/10 calc="AAMATCH(comp,AMINOACID(query,i),AMINOACID(ta
rget,j))"[] 

[24]
Overfull \hbox (32.64503pt too wide) in paragraph at lines 1015--1019
\OT1/cmr/m/n/10 and GE-NOMIC[]INTRON. No-tice how the source lines to and from 
GE-NOMIC[]INSERT

Overfull \hbox (38.24666pt too wide) in paragraph at lines 1116--1116
[]\OT1/cmtt/m/n/10 #define DnaMatrix_Score(dnamat,base1,base2) (dnamat->score[b
ase1][base2])[] 

[25]
Overfull \hbox (11.99689pt too wide) in paragraph at lines 1116--1116
[]  \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,i),GENOMIC_BASE(tar
get,j))"[] 

[26]
[27]
Overfull \hbox (122.24593pt too wide) in paragraph at lines 1335--1335
[]  \OT1/cmtt/m/n/10 fprintf(ofp,"\nest2gen <options> est-seq genomic-seq\nBoth
 sequences in fasta format\n"[] 

[28]
Overfull \hbox (269.24464pt too wide) in paragraph at lines 1335--1335
[]  \OT1/cmtt/m/n/10 if( strip_out_boolean_argument(&argc,argv,"h") == TRUE || 
strip_out_boolean_argument(&argc,argv,"-help") == TRUE) {[] 

[29]
Overfull \hbox (43.49661pt too wide) in paragraph at lines 1335--1335
[]    \OT1/cmtt/m/n/10 warn("Must have two arguments for sequence 1 and sequenc
e 2 %d",argc);[] 

Overfull \hbox (27.74675pt too wide) in paragraph at lines 1335--1335
[]   \OT1/cmtt/m/n/10 * To do this we need a cdna ComplexSequenceEvalSet and a 
genomic one[] 

Overfull \hbox (53.99652pt too wide) in paragraph at lines 1335--1335
[]   \OT1/cmtt/m/n/10 * Really our genomic model should be alot more complex. T
he 'default' one[] 

Overfull \hbox (38.24666pt too wide) in paragraph at lines 1335--1335
[]   \OT1/cmtt/m/n/10 * has 0 at GT----AG for 5' and 3' splice sites, and NEGI 
(= -infinity)[] 

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

Overfull \hbox (43.49661pt too wide) in paragraph at lines 1335--1335
[]   \OT1/cmtt/m/n/10 * other machinery, but not for now <grin>. See the genewi
se code if you[] 

[30]
Overfull \hbox (48.74657pt too wide) in paragraph at lines 1335--1335
[]    \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s
",query->name);[] 

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

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

Overfull \hbox (43.49661pt too wide) in paragraph at lines 1335--1335
[]   \OT1/cmtt/m/n/10 * program. Firstly we are treating errors similarly on ea
ch side of the[] 

Overfull \hbox (59.24648pt too wide) in paragraph at lines 1335--1335
[]   \OT1/cmtt/m/n/10 * Secondly there is a rather complex interaction between 
the gap/extension[] 

Overfull \hbox (53.99652pt too wide) in paragraph at lines 1335--1335
[]   \OT1/cmtt/m/n/10 * of what is thought to be sequencing error and the intro
ns. Here we have[] 

Overfull \hbox (64.49643pt too wide) in paragraph at lines 1335--1335
[]   \OT1/cmtt/m/n/10 * one more parameter, and intron open penalty, which can 
be set, to prevent[] 

Overfull \hbox (48.74657pt too wide) in paragraph at lines 1335--1335
[]   \OT1/cmtt/m/n/10 * One good way to parameterise all this would be to have 
a probabilistic[] 

Overfull \hbox (48.74657pt too wide) in paragraph at lines 1335--1335
[]   \OT1/cmtt/m/n/10 * model of the processes, derive probabilities and then m
ap them to ints[] 

Overfull \hbox (27.74675pt too wide) in paragraph at lines 1335--1335
[]   \OT1/cmtt/m/n/10 * (probability.h has got these mappings, such as Probabil
ity2Score).[] 

Overfull \hbox (101.24611pt too wide) in paragraph at lines 1335--1335
[]  \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_cDNA2Gen(query_cs,target_cs,dm,ga
p,-ext,-gap,-ext,0,NULL);[] 

Overfull \hbox (80.24629pt too wide) in paragraph at lines 1335--1335
[]    \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query
->name,target->name);[] 

[31]
Overfull \hbox (74.99634pt too wide) in paragraph at lines 1342--1342
[]  \OT1/cmtt/m/n/10 pal = PackAln_bestmemory_cDNA2Gen(query_cs,target_cs,dm,ga
p,-ext,-gap,-ext,0);[] 

[32]
Overfull \hbox (27.74675pt too wide) in paragraph at lines 1379--1379
[]   \OT1/cmtt/m/n/10 * To do this we need a cdna ComplexSequenceEvalSet and a 
genomic one[] 

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

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

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

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

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

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

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

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

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

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

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

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

[33]
Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]\OT1/cmtt/m/n/10 HSHNCPA1        98   CAGTGGCAAGAAAAGGGGCTTTGCCT-TAGTAACCTTTG
ACGACCATGA[] 

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

[34]
Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]\OT1/cmtt/m/n/10 HSHNCPA1        482  GTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGG
AGGCAGAAGC[] 

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

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

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

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

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

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

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

Overfull \hbox (22.4968pt too wide) in paragraph at lines 1465--1465
[]\OT1/cmtt/m/n/10 HSHNRNPA        3959 AAG<-3962:4251->GTGGCTATGGCGGTTCCAGCAGC
AGCAGTAGCT[] 

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

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

[36]
[37]
Overfull \hbox (22.4968pt too wide) in paragraph at lines 1600--1600
[]\OT1/cmtt/m/n/10 query  type="MySequence*"  name="query" field:len="length_of
_sequence"[] 

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

Overfull \hbox (127.49588pt too wide) in paragraph at lines 1634--1634
[]      \OT1/cmtt/m/n/10 fprintf(stdout,"%d,%d are matched with score %d\n",uni
t->i+1,unit->j+1,unit->score);[] 

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

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

[39]
[40]
Overfull \hbox (22.4968pt too wide) in paragraph at lines 1849--1849
[]\OT1/cmtt/m/n/10 query  type="MySequence*"  name="query" field:len="length_of
_sequence"[] 

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

[41]
Overfull \hbox (258.74474pt too wide) in paragraph at lines 1849--1849
[]  \OT1/cmtt/m/n/10 calc="ALPHA_SEQ_SCORE(query,i) + ALPHA_SEQ_SCORE(target,j)
 + mat_alpha.comp[SEQ_POS(query,i)][SEQ_POS(target,j)]"[] 

[42]
[43]
Overfull \hbox (20.54509pt too wide) in paragraph at lines 1911--1912
[]\OT1/cmr/m/n/10 The macro Dna-Ma-trix[]Score which is de-fined at the top of 
the cdna2genomic.dy

Overfull \hbox (17.24684pt too wide) in paragraph at lines 1928--1928
[]  \OT1/cmtt/m/n/10 calc="DNA_MAT_SCORE(dm,CDNA_BASE(query,i),GENOMIC_CODON(ta
rget,j))"[] 

[44]
Overfull \hbox (53.99652pt too wide) in paragraph at lines 1944--1944
[]        \OT1/cmtt/m/n/10 Mis-type in argument 3 of DNA\_MAT\_SCORE: wanted [b
ase] got [codon][] 

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

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

Overfull \hbox (11.99689pt too wide) in paragraph at lines 1967--1967
[]\OT1/cmtt/m/n/10 expect to paired directly in a function. This is just a warn
ing that[] 

[45]
Overfull \hbox (17.24684pt too wide) in paragraph at lines 2014--2014
[]  \OT1/cmtt/m/n/10 throw_warning("Letter %c does not exist in comparison matr
ix",one);[] 

Overfull \hbox (17.24684pt too wide) in paragraph at lines 2014--2014
[]  \OT1/cmtt/m/n/10 throw_warning("Letter %c does not exist in comparison matr
ix",two);[] 

[46]
[47]
Overfull \hbox (74.99634pt too wide) in paragraph at lines 2255--2255
[]  \OT1/cmtt/m/n/10 fprintf(stdout,"dbsearch [options] <protein-seq> <protein-
fasta-database>\n");[] 

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

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

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

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

Overfull \hbox (53.99652pt too wide) in paragraph at lines 2255--2255
[]      \OT1/cmtt/m/n/10 is not too likely, and this makes this program future 
proof wrt to new[] 

[48]
Overfull \hbox (43.49661pt too wide) in paragraph at lines 2255--2255
[]   \OT1/cmtt/m/n/10 * care about which implementation is used, and does not k
now either (!)[] 

[49]
Overfull \hbox (106.49606pt too wide) in paragraph at lines 2255--2255
[]  \OT1/cmtt/m/n/10 /* 10 means a score cutoff of 10, -1 means don't report on
 stderr search progress */[] 

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

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

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

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

Overfull \hbox (1.49698pt too wide) in paragraph at lines 2255--2255
[]      \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta
rget);[] 

[50]
Overfull \hbox (74.99634pt too wide) in paragraph at lines 2255--2255
[] \OT1/cmtt/m/n/10 fatal("Unable to make a protein complex sequence from %s",t
emp->baseseq->name);[] 

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

Overfull \hbox (101.24611pt too wide) in paragraph at lines 2255--2255
[] \OT1/cmtt/m/n/10 fatal("Unable to make an alignment from %s and %s",query->n
ame,temp->baseseq->name);[] 

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

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

Overfull \hbox (53.99652pt too wide) in paragraph at lines 2263--2263
[]    \OT1/cmtt/m/n/10 fatal("Some sort of error in the database search. Dieing
 ungracefully");[] 

[51]
Overfull \hbox (1.49698pt too wide) in paragraph at lines 2292--2292
[]      \OT1/cmtt/m/n/10 temp = get_Protein_from_ProteinDB(prodb,out->ds[i]->ta
rget);[] 

[52]
[53]
[54]
[55]
[56]
Overfull \hbox (1.32472pt too wide) in paragraph at lines 2528--2534
\OT1/cmr/m/n/10 de-scribed by a "state...endstate" multi-line block. Within eac
h "state...endstate"

[57]
[58]
[59]
[60]
[61]
Overfull \hbox (1.75064pt too wide) in paragraph at lines 2772--2776
\OT1/cmr/m/n/10 Dy-na-mite file: for ex-am-ple the fol-low-ing er-ror was made 
by mistyp-ing ``MATCH''

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

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

[62]
[63]
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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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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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I+ D+ +GKK[] 

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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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-1>  aaaac[] 

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

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: 2793][] 

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6.


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5.


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.


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66.


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3.


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3.


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e 900.


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

[26]

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n-protein>[] 

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n-protein>[] 

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s introns[] 

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  6[] 

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[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, 213109 bytes).
Transcript written on wise2.log.
cd docs && pdflatex wise2.tex
This is pdfTeX, Version 3.141592653-2.6-1.40.26 (TeX Live 2025/dev/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./wise2.tex
LaTeX2e <2024-11-01> patch level 2
L3 programming layer <2025-01-18>
(/usr/share/texlive/texmf-dist/tex/latex/base/article.cls
Document Class: article 2024/06/29 v1.4n Standard LaTeX document class
(/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphicx.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/keyval.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics/graphics.sty
(/usr/share/texlive/texmf-dist/tex/latex/graphics/trig.sty)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/graphics.cfg)
(/usr/share/texlive/texmf-dist/tex/latex/graphics-def/pdftex.def)))
(/usr/share/texlive/texmf-dist/tex/latex/l3backend/l3backend-pdftex.def)
(./wise2.aux)
(/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
) (/usr/share/texlive/texmf-dist/tex/latex/epstopdf-pkg/epstopdf-base.sty
(/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg))
[1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (./wise2.toc
[2])
[3]
[4]
[5]
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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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       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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[7]
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TAGTTcatca[] 

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-1>  aaaac[] 

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     gactt[] 

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: 2793][] 

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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]
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[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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n-protein>[] 

[30]
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s introns[] 

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

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[43] (./wise2.aux)

LaTeX Warning: There were undefined references.


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

 )
(see the transcript file for additional information) </tmp/texfonts/pk/ljfour/j
knappen/ec/tcrm1000.600pk></usr/share/texlive/texmf-dist/fonts/type1/public/ams
fonts/cm/cmbx10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr
10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr12.pfb>
</usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr17.pfb></usr/s
hare/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/t
exlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmti10.pfb></usr/share/texlive
/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb>
Output written on wise2.pdf (43 pages, 215399 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
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./wise2.tex:263: Warning: \hbox
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./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
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./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 '/build/reproducible-path/wise-2.4.1'
	rm -f debian/wise-data.debhelper.log debian/wise-doc.debhelper.log debian/wise.debhelper.log
   debian/rules override_dh_auto_test
make[1]: Entering directory '/build/reproducible-path/wise-2.4.1'
echo "Since a patch was used to adapt the binaries to the Debian locations of data files the test suite will not run in the build directory any more."
Since a patch was used to adapt the binaries to the Debian locations of data files the test suite will not run in the build directory any more.
echo "A autopkgtest was added as compensation."
A autopkgtest was added as compensation.
# make -C src test
make[1]: Leaving directory '/build/reproducible-path/wise-2.4.1'
   create-stamp debian/debhelper-build-stamp
   dh_prep
	rm -f -- debian/wise.substvars debian/wise-doc.substvars debian/wise-data.substvars
	rm -fr -- debian/.debhelper/generated/wise/ debian/wise/ debian/tmp/ debian/.debhelper/generated/wise-doc/ debian/wise-doc/ debian/.debhelper/generated/wise-data/ debian/wise-data/
   dh_installdirs
	install -m0755 -d debian/wise/usr/bin
	install -m0755 -d debian/wise-data/usr/share/wise
   dh_install
	install -m0755 -d debian/wise/usr/bin
	cp --reflink=auto -a ./src/bin/dba ./src/bin/dnal ./src/bin/estwise ./src/bin/estwisedb ./src/bin/genewise ./src/bin/genewisedb ./src/bin/promoterwise ./src/bin/psw ./src/bin/pswdb ./src/bin/scanwise ./src/bin/scanwise_server ./src/models/genomewise debian/wise/usr/bin/
	install -m0755 -d debian/wise-data/usr/share/wise
	cp --reflink=auto -a ./wisecfg/BLOSUM30.bla ./wisecfg/BLOSUM45.bla ./wisecfg/BLOSUM62.bla ./wisecfg/BLOSUM80.bla ./wisecfg/aa.rnd ./wisecfg/cb.tmf ./wisecfg/codon.martian ./wisecfg/codon.table ./wisecfg/gene.stat ./wisecfg/gon120.bla ./wisecfg/gon160.bla ./wisecfg/gon200.bla ./wisecfg/gon250.bla ./wisecfg/gon350.bla ./wisecfg/human.gf ./wisecfg/human.gp ./wisecfg/human.stats ./wisecfg/idenity.bla ./wisecfg/methods ./wisecfg/pb.gf ./wisecfg/pombe.gf ./wisecfg/tm.pri ./wisecfg/wag55 ./wisecfg/wag65 ./wisecfg/wag75 ./wisecfg/wag85 ./wisecfg/wise.2 ./wisecfg/wise.per ./wisecfg/worm.gf debian/wise-data/usr/share/wise/
   dh_installdocs
	install -m0755 -d debian/wise/usr/share/doc/wise
	install -m0755 -d debian/wise/usr/share/doc/wise
	cp --reflink=auto -a ./README debian/wise/usr/share/doc/wise
	cp --reflink=auto -a ./debian/tests/run-unit-test debian/wise/usr/share/doc/wise
	chmod -R u\+rw,go=rX debian/wise/usr/share/doc
	install -p -m0644 debian/README.Debian debian/wise/usr/share/doc/wise/README.Debian
	install -p -m0644 debian/copyright debian/wise/usr/share/doc/wise/copyright
	install -m0755 -d debian/wise-doc/usr/share/doc/wise-doc
	install -m0755 -d debian/wise-doc/usr/share/doc/wise
	cp --reflink=auto -a ./docs/api.pdf debian/wise-doc/usr/share/doc/wise
	cp --reflink=auto -a ./docs/dynamite.pdf debian/wise-doc/usr/share/doc/wise
	cp --reflink=auto -a ./docs/wise2.pdf debian/wise-doc/usr/share/doc/wise
	cd './docs/api/..' && find 'api' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /build/reproducible-path/wise-2.4.1/debian/wise-doc/usr/share/doc/wise
	cd './docs/dynamite/..' && find 'dynamite' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /build/reproducible-path/wise-2.4.1/debian/wise-doc/usr/share/doc/wise
	cd './docs/wise2/..' && find 'wise2' \( -type f -or -type l \) -and ! -empty -print0 | LC_ALL=C sort -z | xargs -0 -I {} cp --reflink=auto --parents -dp {} /build/reproducible-path/wise-2.4.1/debian/wise-doc/usr/share/doc/wise
	chmod -R u\+rw,go=rX debian/wise-doc/usr/share/doc
	install -p -m0644 debian/copyright debian/wise-doc/usr/share/doc/wise-doc/copyright
	install -m0755 -d debian/wise-doc/usr/share/doc-base/
	install -p -m0644 debian/wise-doc.doc-base.dynamite debian/wise-doc/usr/share/doc-base/wise-doc.wise-dynamite
	install -p -m0644 debian/wise-doc.doc-base.wise debian/wise-doc/usr/share/doc-base/wise-doc.wise
	install -p -m0644 debian/wise-doc.doc-base.api debian/wise-doc/usr/share/doc-base/wise-doc.wise-api
	install -m0755 -d debian/wise-data/usr/share/doc/wise-data
	install -p -m0644 debian/copyright debian/wise-data/usr/share/doc/wise-data/copyright
   dh_installchangelogs
	install -m0755 -d debian/wise-data/usr/share/doc/wise-data
	install -p -m0644 debian/.debhelper/generated/wise-data/dh_installchangelogs.dch.trimmed debian/wise-data/usr/share/doc/wise-data/changelog.Debian
	install -m0755 -d debian/wise/usr/share/doc/wise
	install -p -m0644 debian/.debhelper/generated/wise/dh_installchangelogs.dch.trimmed debian/wise/usr/share/doc/wise/changelog.Debian
	install -m0755 -d debian/wise-doc/usr/share/doc/wise-doc
	install -p -m0644 debian/.debhelper/generated/wise-doc/dh_installchangelogs.dch.trimmed debian/wise-doc/usr/share/doc/wise-doc/changelog.Debian
   debian/rules override_dh_installexamples-indep
make[1]: Entering directory '/build/reproducible-path/wise-2.4.1'
dh_installexamples
	install -m0755 -d debian/wise-data/usr/share/doc/wise-data/examples
	cp --reflink=auto -a ./src/test/basic_cdna.out debian/wise-data/usr/share/doc/wise-data/examples
	cp --reflink=auto -a ./src/test/basic_dna.out debian/wise-data/usr/share/doc/wise-data/examples
	cp --reflink=auto -a ./src/test/basic_genomic.out debian/wise-data/usr/share/doc/wise-data/examples
	cp --reflink=auto -a ./src/test/dna.db debian/wise-data/usr/share/doc/wise-data/examples
	cp --reflink=auto -a ./src/test/estwise-db.out debian/wise-data/usr/share/doc/wise-data/examples
	cp --reflink=auto -a ./src/test/genewise-db-lite.out debian/wise-data/usr/share/doc/wise-data/examples
	cp --reflink=auto -a ./src/test/genewise-db.out debian/wise-data/usr/share/doc/wise-data/examples
	cp --reflink=auto -a ./src/test/genewisedb-pfam.out debian/wise-data/usr/share/doc/wise-data/examples
	cp --reflink=auto -a ./src/test/go.evi debian/wise-data/usr/share/doc/wise-data/examples
	cp --reflink=auto -a ./src/test/go.out debian/wise-data/usr/share/doc/wise-data/examples
	cp --reflink=auto -a ./src/test/HMM.ascii debian/wise-data/usr/share/doc/wise-data/examples
	cp --reflink=auto -a ./src/test/HMM.binary debian/wise-data/usr/share/doc/wise-data/examples
	cp --reflink=auto -a ./src/test/hmm_cdna.out debian/wise-data/usr/share/doc/wise-data/examples
	cp --reflink=auto -a ./src/test/hmm_genomic.out debian/wise-data/usr/share/doc/wise-data/examples
	cp --reflink=auto -a ./src/test/human.genomic debian/wise-data/usr/share/doc/wise-data/examples
	cp --reflink=auto -a ./src/test/pep.fa debian/wise-data/usr/share/doc/wise-data/examples
	cp --reflink=auto -a ./src/test/promoterwise.out debian/wise-data/usr/share/doc/wise-data/examples
	cp --reflink=auto -a ./src/test/pswdb.out debian/wise-data/usr/share/doc/wise-data/examples
	cp --reflink=auto -a ./src/test/pw.human debian/wise-data/usr/share/doc/wise-data/examples
	cp --reflink=auto -a ./src/test/pw.mouse debian/wise-data/usr/share/doc/wise-data/examples
	cp --reflink=auto -a ./src/test/road.pep debian/wise-data/usr/share/doc/wise-data/examples
	cp --reflink=auto -a ./src/test/rrm.HMM debian/wise-data/usr/share/doc/wise-data/examples
	cp --reflink=auto -a ./src/test/scanwisep.out debian/wise-data/usr/share/doc/wise-data/examples
	cp --reflink=auto -a ./src/test/short.dna debian/wise-data/usr/share/doc/wise-data/examples
	cp --reflink=auto -a ./src/test/short.pep debian/wise-data/usr/share/doc/wise-data/examples
	cp --reflink=auto -a ./src/test/short.test debian/wise-data/usr/share/doc/wise-data/examples
	cp --reflink=auto -a ./src/test/testman.pl debian/wise-data/usr/share/doc/wise-data/examples
	cp --reflink=auto -a ./src/test/wrong.hmm debian/wise-data/usr/share/doc/wise-data/examples
	cp --reflink=auto -a ./src/test/wrong.out debian/wise-data/usr/share/doc/wise-data/examples
	cp --reflink=auto -a ./src/test/wrong_est.out debian/wise-data/usr/share/doc/wise-data/examples
sed -i -e 's?"../bin/$do"?"$do"?' -e 's?#!/usr/local/bin/perl?/usr/bin/perl?' debian/wise-data/usr/share/doc/wise-data/examples/testman.pl
make[1]: Leaving directory '/build/reproducible-path/wise-2.4.1'
   dh_installexamples -Nwise-doc -Nwise-data
   dh_installman
	install -m0755 -d debian/wise/usr/share/man/man1/
	install -p -m0644 ./debian/manpages.d/dba.1 debian/wise/usr/share/man/man1/dba.1
	install -m0755 -d debian/wise/usr/share/man/man1/
	install -p -m0644 ./debian/manpages.d/dnal.1 debian/wise/usr/share/man/man1/dnal.1
	install -m0755 -d debian/wise/usr/share/man/man1/
	install -p -m0644 ./debian/manpages.d/estwise.1 debian/wise/usr/share/man/man1/estwise.1
	install -m0755 -d debian/wise/usr/share/man/man1/
	install -p -m0644 ./debian/manpages.d/estwisedb.1 debian/wise/usr/share/man/man1/estwisedb.1
	install -m0755 -d debian/wise/usr/share/man/man1/
	install -p -m0644 ./debian/manpages.d/genewise.1 debian/wise/usr/share/man/man1/genewise.1
	install -m0755 -d debian/wise/usr/share/man/man1/
	install -p -m0644 ./debian/manpages.d/genewisedb.1 debian/wise/usr/share/man/man1/genewisedb.1
	install -m0755 -d debian/wise/usr/share/man/man1/
	install -p -m0644 ./debian/manpages.d/genomewise.1 debian/wise/usr/share/man/man1/genomewise.1
	install -m0755 -d debian/wise/usr/share/man/man1/
	install -p -m0644 ./debian/manpages.d/promoterwise.1 debian/wise/usr/share/man/man1/promoterwise.1
	install -m0755 -d debian/wise/usr/share/man/man1/
	install -p -m0644 ./debian/manpages.d/psw.1 debian/wise/usr/share/man/man1/psw.1
	install -m0755 -d debian/wise/usr/share/man/man1/
	install -p -m0644 ./debian/manpages.d/pswdb.1 debian/wise/usr/share/man/man1/pswdb.1
	install -m0755 -d debian/wise/usr/share/man/man1/
	install -p -m0644 ./debian/manpages.d/scanwise.1 debian/wise/usr/share/man/man1/scanwise.1
	install -m0755 -d debian/wise/usr/share/man/man1/
	install -p -m0644 ./debian/manpages.d/scanwise_server.1 debian/wise/usr/share/man/man1/scanwise_server.1
	man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/dba.1
	man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/dnal.1
	man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/estwise.1
	man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/estwisedb.1
	man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/genomewise.1
	man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/promoterwise.1
	man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/genewise.1
	man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/genewisedb.1
	man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/scanwise.1
	man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/psw.1
	man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/pswdb.1
	man-recode --to-code UTF-8 --suffix .dh-new debian/wise/usr/share/man/man1/scanwise_server.1
	mv debian/wise/usr/share/man/man1/estwise.1.dh-new debian/wise/usr/share/man/man1/estwise.1
	chmod 0644 -- debian/wise/usr/share/man/man1/estwise.1
	mv debian/wise/usr/share/man/man1/dnal.1.dh-new debian/wise/usr/share/man/man1/dnal.1
	chmod 0644 -- debian/wise/usr/share/man/man1/dnal.1
	mv debian/wise/usr/share/man/man1/psw.1.dh-new debian/wise/usr/share/man/man1/psw.1
	chmod 0644 -- debian/wise/usr/share/man/man1/psw.1
	mv debian/wise/usr/share/man/man1/dba.1.dh-new debian/wise/usr/share/man/man1/dba.1
	chmod 0644 -- debian/wise/usr/share/man/man1/dba.1
	mv debian/wise/usr/share/man/man1/genewisedb.1.dh-new debian/wise/usr/share/man/man1/genewisedb.1
	chmod 0644 -- debian/wise/usr/share/man/man1/genewisedb.1
	mv debian/wise/usr/share/man/man1/estwisedb.1.dh-new debian/wise/usr/share/man/man1/estwisedb.1
	chmod 0644 -- debian/wise/usr/share/man/man1/estwisedb.1
	mv debian/wise/usr/share/man/man1/promoterwise.1.dh-new debian/wise/usr/share/man/man1/promoterwise.1
	chmod 0644 -- debian/wise/usr/share/man/man1/promoterwise.1
	mv debian/wise/usr/share/man/man1/genewise.1.dh-new debian/wise/usr/share/man/man1/genewise.1
	chmod 0644 -- debian/wise/usr/share/man/man1/genewise.1
	mv debian/wise/usr/share/man/man1/pswdb.1.dh-new debian/wise/usr/share/man/man1/pswdb.1
	chmod 0644 -- 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
	chmod 0644 -- 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/scanwise_server.1
	mv debian/wise/usr/share/man/man1/genomewise.1.dh-new debian/wise/usr/share/man/man1/genomewise.1
	chmod 0644 -- debian/wise/usr/share/man/man1/genomewise.1
   dh_perl
   dh_link
   dh_strip_nondeterminism
   dh_compress
	cd debian/wise-data
	cd debian/wise-doc
	cd debian/wise
	chmod a-x usr/share/doc/wise-doc/changelog.Debian usr/share/doc/wise/api.pdf usr/share/doc/wise/dynamite.pdf usr/share/doc/wise/wise2.pdf
	gzip -9nf usr/share/doc/wise-doc/changelog.Debian usr/share/doc/wise/api.pdf usr/share/doc/wise/dynamite.pdf usr/share/doc/wise/wise2.pdf
	chmod a-x usr/share/doc/wise-data/changelog.Debian
	gzip -9nf usr/share/doc/wise-data/changelog.Debian
	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
	cd '/build/reproducible-path/wise-2.4.1'
	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 '/build/reproducible-path/wise-2.4.1'
	cd '/build/reproducible-path/wise-2.4.1'
	rm -f debian/wise-data.debhelper.log debian/wise-doc.debhelper.log
   debian/rules override_dh_fixperms
make[1]: Entering directory '/build/reproducible-path/wise-2.4.1'
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-data ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
	find debian/wise-doc ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
	find debian/wise-doc/usr/share/doc -type f -a -true -a ! -regex 'debian/wise-doc/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
	find debian/wise-data/usr/share/doc -type f -a -true -a ! -regex 'debian/wise-data/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
	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-doc/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
	find debian/wise-data/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
	find debian/wise/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755
	find debian/wise-data -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-doc -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/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 '/build/reproducible-path/wise-2.4.1'
   dh_missing
   dh_dwz -a
	install -m0755 -d debian/wise/usr/lib/debug/.dwz/x86_64-linux-gnu
	dwz -mdebian/wise/usr/lib/debug/.dwz/x86_64-linux-gnu/wise.debug -M/usr/lib/debug/.dwz/x86_64-linux-gnu/wise.debug -- debian/wise/usr/bin/dba debian/wise/usr/bin/dnal debian/wise/usr/bin/estwise debian/wise/usr/bin/estwisedb debian/wise/usr/bin/genewise debian/wise/usr/bin/genewisedb debian/wise/usr/bin/genomewise debian/wise/usr/bin/promoterwise debian/wise/usr/bin/psw debian/wise/usr/bin/pswdb debian/wise/usr/bin/scanwise debian/wise/usr/bin/scanwise_server
	objcopy --compress-debug-sections debian/wise/usr/lib/debug/.dwz/x86_64-linux-gnu/wise.debug
	chmod 0644 -- debian/wise/usr/lib/debug/.dwz/x86_64-linux-gnu/wise.debug
   dh_strip -a
	install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/76
	objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genewise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/76/c74e3e3fdd0bb25887022bc7cdbacf56a96ff5.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/76/c74e3e3fdd0bb25887022bc7cdbacf56a96ff5.debug
	strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genewise
	objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/76/c74e3e3fdd0bb25887022bc7cdbacf56a96ff5.debug debian/wise/usr/bin/genewise
	install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/07
	objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/scanwise_server debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/07/9d5a6e5a0ce0c8a3ed39982eb649968c646d22.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/07/9d5a6e5a0ce0c8a3ed39982eb649968c646d22.debug
	strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/scanwise_server
	objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/07/9d5a6e5a0ce0c8a3ed39982eb649968c646d22.debug debian/wise/usr/bin/scanwise_server
	install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e9
	objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/estwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e9/81b8f629ea2027febaa5caf4f45fab7b26fdc2.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e9/81b8f629ea2027febaa5caf4f45fab7b26fdc2.debug
	strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/estwise
	objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/e9/81b8f629ea2027febaa5caf4f45fab7b26fdc2.debug debian/wise/usr/bin/estwise
	install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/8b
	objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/psw debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/8b/a1da17c9fa2608d2efad9c49a17eda4ae2c248.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/8b/a1da17c9fa2608d2efad9c49a17eda4ae2c248.debug
	strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/psw
	objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/8b/a1da17c9fa2608d2efad9c49a17eda4ae2c248.debug debian/wise/usr/bin/psw
	install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b2
	objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/scanwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b2/cfd039f4b5c2c3322bdd6d1ce5f7dda764312d.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b2/cfd039f4b5c2c3322bdd6d1ce5f7dda764312d.debug
	strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/scanwise
	objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b2/cfd039f4b5c2c3322bdd6d1ce5f7dda764312d.debug debian/wise/usr/bin/scanwise
	install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/da
	objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genewisedb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/da/0a6b4ff7e8c7e75d66ea075a0060a26dbef12a.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/da/0a6b4ff7e8c7e75d66ea075a0060a26dbef12a.debug
	strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genewisedb
	objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/da/0a6b4ff7e8c7e75d66ea075a0060a26dbef12a.debug debian/wise/usr/bin/genewisedb
	install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/71
	objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/pswdb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/71/bed81c42b18899c7f95c58cebd9b1fe1757901.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/71/bed81c42b18899c7f95c58cebd9b1fe1757901.debug
	strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/pswdb
	objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/71/bed81c42b18899c7f95c58cebd9b1fe1757901.debug debian/wise/usr/bin/pswdb
	install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b0
	objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/estwisedb debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b0/8d9e4cd3a7917c950168f89ea6600f3e57b30b.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b0/8d9e4cd3a7917c950168f89ea6600f3e57b30b.debug
	strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/estwisedb
	objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/b0/8d9e4cd3a7917c950168f89ea6600f3e57b30b.debug debian/wise/usr/bin/estwisedb
	install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/ec
	objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/promoterwise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/ec/ed32d8309f7db0a3781f21a4438709986a14cc.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/ec/ed32d8309f7db0a3781f21a4438709986a14cc.debug
	strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/promoterwise
	objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/ec/ed32d8309f7db0a3781f21a4438709986a14cc.debug debian/wise/usr/bin/promoterwise
	install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/37
	objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/genomewise debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/37/03ce9069d93d1de8fd10d61a0f400c072e2286.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/37/03ce9069d93d1de8fd10d61a0f400c072e2286.debug
	strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/genomewise
	objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/37/03ce9069d93d1de8fd10d61a0f400c072e2286.debug debian/wise/usr/bin/genomewise
	install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/08
	objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/dnal debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/08/8a7890e21636ac4f2f8da5a09c2eaeecdf5afd.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/08/8a7890e21636ac4f2f8da5a09c2eaeecdf5afd.debug
	strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/dnal
	objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/08/8a7890e21636ac4f2f8da5a09c2eaeecdf5afd.debug debian/wise/usr/bin/dnal
	install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/45
	objcopy --only-keep-debug --compress-debug-sections debian/wise/usr/bin/dba debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/45/c1055d3673bc15d240d26700bd6e22e74166d4.debug
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/45/c1055d3673bc15d240d26700bd6e22e74166d4.debug
	strip --remove-section=.comment --remove-section=.note debian/wise/usr/bin/dba
	objcopy --add-gnu-debuglink debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.build-id/45/c1055d3673bc15d240d26700bd6e22e74166d4.debug debian/wise/usr/bin/dba
	install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.dwz
	cp --reflink=auto -a debian/wise/usr/lib/debug/.dwz/x86_64-linux-gnu debian/.debhelper/wise/dbgsym-root/usr/lib/debug/.dwz
	rm -fr debian/wise/usr/lib/debug/.dwz
	rmdir -p --ignore-fail-on-non-empty debian/wise/usr/lib/debug
	install -m0755 -d debian/.debhelper/wise/dbgsym-root/usr/share/doc
	ln -s wise debian/.debhelper/wise/dbgsym-root/usr/share/doc/wise-dbgsym
	install -m0755 -d debian/.debhelper/wise
   dh_makeshlibs -a
	rm -f debian/wise/DEBIAN/shlibs
   dh_shlibdeps -a
	install -m0755 -d debian/wise/DEBIAN
	dpkg-shlibdeps -Tdebian/wise.substvars debian/wise/usr/bin/genewise debian/wise/usr/bin/scanwise_server debian/wise/usr/bin/estwise debian/wise/usr/bin/psw debian/wise/usr/bin/scanwise debian/wise/usr/bin/genewisedb debian/wise/usr/bin/pswdb debian/wise/usr/bin/estwisedb debian/wise/usr/bin/promoterwise debian/wise/usr/bin/genomewise debian/wise/usr/bin/dnal debian/wise/usr/bin/dba
   dh_installdeb
	install -m0755 -d debian/wise/DEBIAN
	install -m0755 -d debian/wise-doc/DEBIAN
	install -m0755 -d debian/wise-data/DEBIAN
   dh_gencontrol
	install -m0755 -d debian/wise-doc/DEBIAN
	echo misc:Depends= >> debian/wise-doc.substvars
	echo misc:Pre-Depends= >> debian/wise-doc.substvars
	dpkg-gencontrol -pwise-doc -ldebian/changelog -Tdebian/wise-doc.substvars -cdebian/control -Pdebian/wise-doc
	install -m0755 -d debian/wise-data/DEBIAN
	echo misc:Depends= >> debian/wise-data.substvars
	echo misc:Pre-Depends= >> debian/wise-data.substvars
	dpkg-gencontrol -pwise-data -ldebian/changelog -Tdebian/wise-data.substvars -cdebian/control -Pdebian/wise-data
	install -m0755 -d debian/wise/DEBIAN
	echo misc:Depends= >> debian/wise.substvars
	echo misc:Pre-Depends= >> debian/wise.substvars
	install -m0755 -d debian/.debhelper/wise/dbgsym-root/DEBIAN
	dpkg-gencontrol -pwise -ldebian/changelog -Tdebian/wise.substvars -cdebian/control -Pdebian/.debhelper/wise/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -DAuto-Built-Package=debug-symbols -UProtected -UBuilt-Using -UStatic-Built-Using -DPackage=wise-dbgsym "-DDepends=wise (= \${binary:Version})" "-DDescription=debug symbols for wise" "-DBuild-Ids=079d5a6e5a0ce0c8a3ed39982eb649968c646d22 088a7890e21636ac4f2f8da5a09c2eaeecdf5afd 3703ce9069d93d1de8fd10d61a0f400c072e2286 45c1055d3673bc15d240d26700bd6e22e74166d4 71bed81c42b18899c7f95c58cebd9b1fe1757901 76c74e3e3fdd0bb25887022bc7cdbacf56a96ff5 8ba1da17c9fa2608d2efad9c49a17eda4ae2c248 b08d9e4cd3a7917c950168f89ea6600f3e57b30b b2cfd039f4b5c2c3322bdd6d1ce5f7dda764312d da0a6b4ff7e8c7e75d66ea075a0060a26dbef12a e981b8f629ea2027febaa5caf4f45fab7b26fdc2 eced32d8309f7db0a3781f21a4438709986a14cc" -DSection=debug -UMulti-Arch -UReplaces -UBreaks
	chmod 0644 -- debian/wise-data/DEBIAN/control
	chmod 0644 -- debian/wise-doc/DEBIAN/control
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/DEBIAN/control
	dpkg-gencontrol -pwise -ldebian/changelog -Tdebian/wise.substvars -cdebian/control -Pdebian/wise
	chmod 0644 -- debian/wise/DEBIAN/control
   dh_md5sums
	install -m0755 -d debian/wise-doc/DEBIAN
	install -m0755 -d debian/wise/DEBIAN
	install -m0755 -d debian/wise-data/DEBIAN
	cd debian/wise-doc >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	cd debian/wise-data >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	cd debian/wise >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	chmod 0644 -- debian/wise-data/DEBIAN/md5sums
	chmod 0644 -- debian/wise-doc/DEBIAN/md5sums
	chmod 0644 -- debian/wise/DEBIAN/md5sums
	install -m0755 -d debian/.debhelper/wise/dbgsym-root/DEBIAN
	cd debian/.debhelper/wise/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums
	chmod 0644 -- debian/.debhelper/wise/dbgsym-root/DEBIAN/md5sums
   dh_builddeb
	dpkg-deb --root-owner-group --build debian/wise ..
	dpkg-deb --root-owner-group --build debian/wise-doc ..
	dpkg-deb --root-owner-group --build debian/.debhelper/wise/dbgsym-root ..
	dpkg-deb --root-owner-group --build debian/wise-data ..
dpkg-deb: building package 'wise-data' in '../wise-data_2.4.1-27_all.deb'.
dpkg-deb: building package 'wise' in '../wise_2.4.1-27_amd64.deb'.
dpkg-deb: building package 'wise-dbgsym' in '../wise-dbgsym_2.4.1-27_amd64.deb'.
dpkg-deb: building package 'wise-doc' in '../wise-doc_2.4.1-27_all.deb'.
 dpkg-genbuildinfo --build=binary -O../wise_2.4.1-27_amd64.buildinfo
 dpkg-genchanges --build=binary -O../wise_2.4.1-27_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env 
I: removing directory /srv/workspace/pbuilder/900143 and its subdirectories
I: Current time: Wed Apr 29 18:31:17 -12 2026
I: pbuilder-time-stamp: 1777530677
Fri Mar 28 00:08:19 UTC 2025  I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net.
Fri Mar 28 00:08:19 UTC 2025  I: Preparing to do remote build '2' on ionos11-amd64.debian.net.
Fri Mar 28 00:14:02 UTC 2025  I: Deleting $TMPDIR on ionos11-amd64.debian.net.
Fri Mar 28 00:14:03 UTC 2025  I: wise_2.4.1-27_amd64.changes:
Format: 1.8
Date: Thu, 27 Mar 2025 20:42:30 +0700
Source: wise
Binary: wise wise-data wise-dbgsym wise-doc
Architecture: all amd64
Version: 2.4.1-27
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Lance Lin <lq27267@gmail.com>
Description:
 wise       - comparison of biopolymers, like DNA and protein sequences
 wise-data  - data files for the wise package
 wise-doc   - documentation for the wise package
Changes:
 wise (2.4.1-27) unstable; urgency=medium
 .
   * Team upload.
   * d/patches: Add patch to fix FTBFS with GCC-15
Checksums-Sha1:
 5e41f287a0583c14057830342e477b9ce8c6564d 76196 wise-data_2.4.1-27_all.deb
 a0e3c5d0e06cf5ad9c8c1c94567ce5f892f90246 8179576 wise-dbgsym_2.4.1-27_amd64.deb
 22e162c8259a6bfe89216f5cdb11f5ef0d5938ab 827768 wise-doc_2.4.1-27_all.deb
 f4d94f3cc3761b004bec16443085b51cbaef8340 10626 wise_2.4.1-27_amd64.buildinfo
 8ea6a004b3953d28c9f53caab6d788df0edde711 1064740 wise_2.4.1-27_amd64.deb
Checksums-Sha256:
 6d6f67209db695a1296e0aecaa222333e6eb87433bbd65898447c1f50ebd7d8b 76196 wise-data_2.4.1-27_all.deb
 9801a1620111624f8845ccd73e4dec94ec8616e16fc2f03b054574541623f770 8179576 wise-dbgsym_2.4.1-27_amd64.deb
 9f2abf86f184ee16abe15b8256358617f766c0fe9422cb456f8cf3af6547fefe 827768 wise-doc_2.4.1-27_all.deb
 6d5e1fab46722b40e533f5ce1bdce5ea2d2389a2bffd09c49710f3b9fc009436 10626 wise_2.4.1-27_amd64.buildinfo
 7572cf1cbc958b22f466f3d4677d830f1841653464b0184f3332dfe247165e55 1064740 wise_2.4.1-27_amd64.deb
Files:
 de7ba0d0f67ece5d015a96f3e9b2de72 76196 doc optional wise-data_2.4.1-27_all.deb
 b27f03d354a7c22ec1490b54514dd07a 8179576 debug optional wise-dbgsym_2.4.1-27_amd64.deb
 6ad813eb363dcc6381b5a9f5236c42d8 827768 doc optional wise-doc_2.4.1-27_all.deb
 f25d9548c49bd7a82899bbc86a5453cf 10626 science optional wise_2.4.1-27_amd64.buildinfo
 7880c674403a81279e2536a008f26e8c 1064740 science optional wise_2.4.1-27_amd64.deb
Fri Mar 28 00:14:04 UTC 2025  I: diffoscope 291 will be used to compare the two builds:
Running as unit: rb-diffoscope-amd64_8-52279.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.ahawirbV/wise_2.4.1-27.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.ahawirbV/wise_2.4.1-27.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.ahawirbV/wise_2.4.1-27.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.ahawirbV/b1/wise_2.4.1-27_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.ahawirbV/b2/wise_2.4.1-27_amd64.changes

## command (total time: 0.000s)
       0.000s      1 call     cmp (internal)

## has_same_content_as (total time: 0.000s)
       0.000s      1 call     diffoscope.comparators.binary.FilesystemFile

## main (total time: 0.003s)
       0.003s      2 calls    outputs
       0.000s      1 call     cleanup
Finished with result: success
Main processes terminated with: code=exited/status=0
Service runtime: 232ms
CPU time consumed: 227ms
Fri Mar 28 00:14:05 UTC 2025  I: diffoscope 291 found no differences in the changes files, and a .buildinfo file also exists.
Fri Mar 28 00:14:05 UTC 2025  I: wise from unstable built successfully and reproducibly on amd64.
Fri Mar 28 00:14:06 UTC 2025  I: Submitting .buildinfo files to external archives:
Fri Mar 28 00:14:06 UTC 2025  I: Submitting 12K	b1/wise_2.4.1-27_amd64.buildinfo.asc
Fri Mar 28 00:14:06 UTC 2025  I: Submitting 12K	b2/wise_2.4.1-27_amd64.buildinfo.asc
Fri Mar 28 00:14:07 UTC 2025  I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Fri Mar 28 00:14:07 UTC 2025  I: Done submitting .buildinfo files.
Fri Mar 28 00:14:07 UTC 2025  I: Removing signed wise_2.4.1-27_amd64.buildinfo.asc files:
removed './b1/wise_2.4.1-27_amd64.buildinfo.asc'
removed './b2/wise_2.4.1-27_amd64.buildinfo.asc'